Shipping method in cart using "template includes"

The shipping options do not populate the select box.

Debug Message - Perch 3.0.14
[1] SELECT * FROM perch3_pages WHERE pagePath='/shop/cart.php' LIMIT 1
[1] SELECT * FROM perch3_shop_cart WHERE cartID=101
[1] SELECT * FROM perch3_shop_cart WHERE cartID=101
[47] SELECT DISTINCT settingID, settingValue FROM perch3_settings WHERE userID=0
[1] SELECT * FROM perch3_shop_products WHERE productID='695' AND productDeleted IS NULL LIMIT 1
[3] SELECT valueSKUCode FROM perch3_shop_option_values WHERE valueID IN ('15', '1', '9') AND optionID IN (5, 1, 3)
[1] SELECT productID FROM perch3_shop_products WHERE parentID=695 AND productDeleted IS NULL AND (sku REGEXP "[[:<:]]XSM[[:>:]]") AND (sku REGEXP "[[:<:]]BLC[[:>:]]") AND (sku REGEXP "[[:<:]]MEN[[:>:]]") LIMIT 1
[1] SELECT itemID, itemQty FROM perch3_shop_cart_items WHERE cartID=101 AND productID=696
[1] SELECT * FROM perch3_shop_products WHERE productID=696 AND productDeleted IS NULL LIMIT 1
INSERT INTO perch3_shop_cart_items(productID,itemQty,cartID) VALUES('696','1','101')
------------------------------ Calculating cart ------------------------------
[1] SELECT * FROM perch3_shop_cart WHERE cartID=101
[1] SELECT * FROM perch3_shop_cart WHERE cartID=101
[1] SELECT * FROM perch3_shop_tax_locations WHERE locationID=1 AND locationDeleted IS NULL LIMIT 1
[1] SELECT locationID FROM perch3_shop_tax_locations WHERE locationIsHome=1 LIMIT 1
[1] SELECT * FROM perch3_shop_tax_locations WHERE locationID=1 AND locationDeleted IS NULL LIMIT 1
[1] SELECT * FROM perch3_shop_currencies WHERE currencyID=142 LIMIT 1
[1] SELECT COUNT(productID) AS product_count, SUM(itemQty) AS item_count FROM perch3_shop_cart_items WHERE cartID=101
Tax mode: exc
[1] SELECT * FROM perch3_shop_cart_items WHERE cartID=101 ORDER BY itemID ASC
[1] SELECT * FROM perch3_shop_products WHERE productID=696 AND productDeleted IS NULL LIMIT 1
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[36] SELECT productID, productVariantDesc, stock_level FROM perch3_shop_products WHERE parentID=695 AND productDeleted IS NULL ORDER BY productOrder ASC
[3] SELECT o.* FROM perch3_shop_options o, perch3_shop_product_options po WHERE o.optionID=po.optionID AND po.productID=695 AND o.optionDeleted IS NULL ORDER BY optionPrecendence ASC
[2] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=5 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[2] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='5' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[6] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=1 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[6] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='1' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[3] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=3 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[3] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='3' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[1] SELECT * FROM perch3_shop_tax_groups WHERE groupID=1 AND groupDeleted IS NULL LIMIT 1
[1] SELECT r.rateValue FROM perch3_shop_tax_group_rates gr, perch3_shop_tax_rates r WHERE gr.rateID=r.rateID AND gr.groupID=1 AND gr.locationID=1
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[1] SELECT * FROM perch3_shop_tax_groups WHERE groupID=1 AND groupDeleted IS NULL LIMIT 1
[1] SELECT r.rateValue FROM perch3_shop_tax_group_rates gr, perch3_shop_tax_rates r WHERE gr.rateID=r.rateID AND gr.groupID=1 AND gr.locationID=1
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[36] SELECT productID, productVariantDesc, stock_level FROM perch3_shop_products WHERE parentID=695 AND productDeleted IS NULL ORDER BY productOrder ASC
[3] SELECT o.* FROM perch3_shop_options o, perch3_shop_product_options po WHERE o.optionID=po.optionID AND po.productID=695 AND o.optionDeleted IS NULL ORDER BY optionPrecendence ASC
[2] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=5 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[2] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='5' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[6] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=1 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[6] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='1' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[3] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=3 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[3] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='3' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[36] SELECT productID, productVariantDesc, stock_level FROM perch3_shop_products WHERE parentID=695 AND productDeleted IS NULL ORDER BY productOrder ASC
[3] SELECT o.* FROM perch3_shop_options o, perch3_shop_product_options po WHERE o.optionID=po.optionID AND po.productID=695 AND o.optionDeleted IS NULL ORDER BY optionPrecendence ASC
[2] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=5 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[2] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='5' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[6] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=1 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[6] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='1' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[3] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=3 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[3] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='3' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[36] SELECT productID, productVariantDesc, stock_level FROM perch3_shop_products WHERE parentID=695 AND productDeleted IS NULL ORDER BY productOrder ASC
[3] SELECT o.* FROM perch3_shop_options o, perch3_shop_product_options po WHERE o.optionID=po.optionID AND po.productID=695 AND o.optionDeleted IS NULL ORDER BY optionPrecendence ASC
[2] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=5 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[2] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='5' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[6] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=1 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[6] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='1' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[3] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=3 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[3] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='3' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[36] SELECT productID, productVariantDesc, stock_level FROM perch3_shop_products WHERE parentID=695 AND productDeleted IS NULL ORDER BY productOrder ASC
[3] SELECT o.* FROM perch3_shop_options o, perch3_shop_product_options po WHERE o.optionID=po.optionID AND po.productID=695 AND o.optionDeleted IS NULL ORDER BY optionPrecendence ASC
[2] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=5 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[2] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='5' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[6] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=1 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[6] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='1' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[3] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=3 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[3] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='3' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[36] SELECT productID, productVariantDesc, stock_level FROM perch3_shop_products WHERE parentID=695 AND productDeleted IS NULL ORDER BY productOrder ASC
[3] SELECT o.* FROM perch3_shop_options o, perch3_shop_product_options po WHERE o.optionID=po.optionID AND po.productID=695 AND o.optionDeleted IS NULL ORDER BY optionPrecendence ASC
[2] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=5 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[2] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='5' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[6] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=1 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[6] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='1' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[3] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=3 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[3] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='3' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[1] SELECT z.* FROM perch3_shop_shipping_zones z LEFT JOIN perch3_shop_shipping_zone_countries c ON z.zoneID=c.zoneID WHERE z.zoneActive=1 AND z.zoneDeleted IS NULL AND (c.countryID=237 OR zoneIsDefault=1) ORDER BY zoneIsDefault ASC LIMIT 1
[2] SELECT * FROM perch3_shop_shippings WHERE shippingDeleted IS NULL ORDER BY shippingOrder ASC
[1] SELECT * FROM perch3_shop_shipping_zones WHERE zoneDeleted IS NULL AND zoneActive=1 AND zoneID IN (1)
[2] SELECT rateID AS id, rateTitle AS title, rateValue AS rate, locationID FROM perch3_shop_tax_rates WHERE rateDeleted IS NULL ORDER BY rateValue DESC
[1] SELECT * FROM perch3_shop_shipping_zones WHERE zoneDeleted IS NULL AND zoneActive=1 AND zoneID IN (1)
Qualifying shipping method ‘Free’
Qualifying shipping method ‘Overnight’
[1] SELECT * FROM perch3_shop_shippings WHERE shippingID='2' AND shippingDeleted IS NULL LIMIT 1
Using shipping zone: USA
[1] SELECT * FROM perch3_shop_tax_groups WHERE groupID=1 AND groupDeleted IS NULL LIMIT 1
[1] SELECT r.rateValue FROM perch3_shop_tax_group_rates gr, perch3_shop_tax_rates r WHERE gr.rateID=r.rateID AND gr.groupID=1 AND gr.locationID=1
[1] SELECT * FROM perch3_shop_promotions WHERE promoFrom<='2018-03-26 17:41:00' AND promoTo>'2018-03-26 17:41:00' AND promoActive=1 AND promoDeleted IS NULL ORDER BY promoOrder ASC
Promo (Jojola Discount) skipped: discount code not applied.
UPDATE perch3_shop_cart SET cartTotalItems='1', cartTotalProducts='1', cartTotalWithTax='16.63', cartTotalWithoutTax='15.99' WHERE cartID='101'
INSERT INTO perch3_shop_cart_data(cartID,productID,cartData) VALUES('101','695','{\"opt-5\":\"15\",\"opt-1\":\"1\",\"opt-3\":\"9\",\"qty\":\"1\",\"product\":\"695\"}')
[6] SELECT * FROM perch3_pages WHERE pageNew=0 AND pageHidden=0 ORDER BY pageTreePosition ASC
[0] SELECT pageTreePosition FROM perch3_pages WHERE pagePath='/shop/cart.php' LIMIT 1
[6] Using template: /templates/navigation/navigation.html
[1] SELECT * FROM perch3_shop_products WHERE productID=695 AND productDeleted IS NULL LIMIT 1
[36] SELECT productID, productVariantDesc, stock_level FROM perch3_shop_products WHERE parentID=695 AND productDeleted IS NULL ORDER BY productOrder ASC
[3] SELECT o.* FROM perch3_shop_options o, perch3_shop_product_options po WHERE o.optionID=po.optionID AND po.productID=695 AND o.optionDeleted IS NULL ORDER BY optionPrecendence ASC
[2] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=5 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[2] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='5' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[6] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=1 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[6] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='1' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
[3] SELECT valueID AS id, valueTitle AS title, valueSKUCode AS skucode FROM perch3_shop_option_values WHERE optionID=3 AND valueDeleted IS NULL ORDER BY valueOrder ASC
[3] SELECT pov.prodoptID, pov.optionID, pov.valueID, o.optionTitle, ov.* FROM perch3_shop_product_option_values pov, perch3_shop_options o, perch3_shop_option_values ov WHERE pov.productID='695' AND pov.optionID=o.optionID AND pov.valueID=ov.valueID AND o.optionDeleted IS NULL AND ov.valueDeleted IS NULL AND o.optionID='3' ORDER BY o.optionPrecendence ASC, ov.valueOrder ASC
Using template: /addons/apps/perch_shop/templates/shop/cart/cart.html
[3] Using sub-template: /templates/content/method_form.html

Here is what's on my page.

<?php include('../admin/runtime.php'); ?>
<!DOCTYPE html>
<html dir="ltr" lang="en-US">
    <head>
        <?php
            perch_page_attributes(array(
            'template'=>'seo.html'
            ));
            perch_layout('global.stylesheet');
        ?>
        <link rel="stylesheet" href="https://canvashtml-cdn.semicolonweb.com/v5/css/components/bs-select.css" type="text/css" />
        <link rel="stylesheet" href="https://canvashtml-cdn.semicolonweb.com/v5/css/responsive.css" type="text/css" />
    </head>
    <body class="stretched">        
        <div id="wrapper" class="clearfix">
            <header id="header" class="full-header">
                <div id="header-wrap">
                    <div class="container clearfix">
                        <div id="primary-menu-trigger"><i class="icon-reorder"></i></div>
                        <?php perch_layout('global.navlogo'); ?>
                        <?php
                            perch_pages_navigation(array(
                                'template' => array('navigation.html'),
                            ));
                        ?>
                    </div>
                </div>
            </header>
            <section id="page-title">
                <div class="container clearfix">
                    <h1>Cart</h1>
                    <ol class="breadcrumb">
                        <li class="breadcrumb-item"><a href="/index.php">Home</a></li>
                        <li class="breadcrumb-item"><a href="/shop">Shop</a></li>
                        <li class="breadcrumb-item active" aria-current="page">Cart</li>
                    </ol>
                </div>
            </section>
            <?php perch_shop_cart(); ?>
            <footer id="footer" class="dark">
                <?php perch_layout('global.footer'); ?>
                <?php perch_content('Copyrights'); ?>
            </footer>
        </div>
        <div id="gotoTop" class="icon-angle-up"></div>
        <?php perch_layout('global.script'); ?>
        <script>
            jQuery(document).ready( function($){
                $('#shop').isotope({
                    transitionDuration: '0.65s',
                    getSortData: {
                        name: '.product-title',
                        price_lh: function( itemElem ) {
                            if( $(itemElem).find('.product-price').find('ins').length > 0 ) {
                                var price = $(itemElem).find('.product-price ins').text();
                            } else {
                                var price = $(itemElem).find('.product-price').text();
                            }

                            priceNum = price.split("$");

                            return parseFloat( priceNum[1] );
                        },
                        price_hl: function( itemElem ) {
                            if( $(itemElem).find('.product-price').find('ins').length > 0 ) {
                                var price = $(itemElem).find('.product-price ins').text();
                            } else {
                                var price = $(itemElem).find('.product-price').text();
                            }

                            priceNum = price.split("$");

                            return parseFloat( priceNum[1] );
                        }
                    },
                    sortAscending: {
                        name: true,
                        price_lh: true,
                        price_hl: false
                    }
                });

                $('.custom-filter:not(.no-count)').children('li:not(.widget-filter-reset)').each( function(){
                    var element = $(this),
                        elementFilter = element.children('a').attr('data-filter'),
                        elementFilterContainer = element.parents('.custom-filter').attr('data-container');

                    elementFilterCount = Number( jQuery(elementFilterContainer).find( elementFilter ).length );

                    element.append('<span>'+ elementFilterCount +'</span>');

                });

                $('.shop-sorting li').click( function() {
                    $('.shop-sorting').find('li').removeClass( 'active-filter' );
                    $(this).addClass( 'active-filter' );
                    var sortByValue = $(this).find('a').attr('data-sort-by');
                    $('#shop').isotope({ sortBy: sortByValue });
                    return false;
                });
            });
        </script>
        <script src="https://canvashtml-cdn.semicolonweb.com/v5/js/components/bs-select.js"></script>
        <script src="https://canvashtml-cdn.semicolonweb.com/v5/js/components/selectsplitter.js"></script>
        <script src="https://canvashtml-cdn.semicolonweb.com/v5/js/functions.js"></script>
        <script>
            $('.selectsplitter').selectsplitter();
        </script>
    </body>
</html>

This is "method_form.html"

<perch:form id="shipping_method" method="post" app="perch_shop">
    <h4>Shipping method</h4>

    <perch:error for="all" type="login">
        <p class="error">Sorry, there was a problem.</p>
    </perch:error>

    <div>
        <perch:label for="shipping">Method</perch:label>
        <perch:input type="select" options="<perch:shop id="shippings_list" />" id="shipping" required="true" placeholder="Please choose"  />
        <perch:error for="shipping" type="required">Required</perch:error>
    </div>
    <div>
        <perch:input type="submit" id="submit" value="OK!" />
        <perch:input type="hidden" id="r" />
    </div>

</perch:form>

Hello Justin,

What you have at the moment is:

<perch:form id="cart" app="perch_shop">
.
.
<perch:form id="shipping_method" method="post" app="perch_shop">
</perch:form>
.
.
</perch:form>

Even if Perch renders the inner form correctly (use your browser dev tools to check), I'm not sure that's going to work as <form> elements aren't supposed to have other <form> elements inside them. See HTML5 docs:

Flow content, but with no form element descendants.

I removed the "template include". Instead just placed the code in the template. When I debug I see the options.

SELECT * FROM perch3_shop_shipping_zones WHERE zoneDeleted IS NULL AND zoneActive=1 AND zoneID IN (1)
Qualifying shipping method ‘Free’
Qualifying shipping method ‘Overnight’
[1] SELECT * FROM perch3_shop_shippings WHERE shippingID='2' AND shippingDeleted IS NULL LIMIT 1
Using shipping zone: USA

If I view the source code from the browser the options are not there. ~~ <div> <select id="form1_shipping" name="shipping" class="selectpicker" placeholder="Please choose" required="required"><option disabled="disabled" selected="selected" value="">Please choose</option><option selected="selected" value=""></option></select>

                                                <input id="form1_submit" name="submit" class="button button-3d notopmargin fright" value="OK!" type="submit"><input type="hidden" name="cms-form" value="Y2FydDpwZXJjaF9zaG9wOi9hZGRvbnMvYXBwcy9wZXJjaF9zaG9wL3RlbXBsYXRlcy9zaG9wL2NhcnQvY2FydC5odG1sOjE1MjIxNjIwOTI=">
                                                <input id="form1_r" name="r" type="hidden">
                                            </div>

~~

Here is the template I'm using.

<section id="content">
    <div class="content-wrap">
        <div class="container clearfix">
            <perch:if id="product_count" match="gt" value="0">
                <perch:form id="cart" app="perch_shop">
                    <perch:input type="submit" value="Update" hidden="true" aria-hidden="true" />
                    <div class="table-responsive">
                        <table class="table cart">
                            <thead>
                                <tr>
                                    <th class="cart-product-remove" style="width:100px">&nbsp;</th>
                                    <th class="cart-product-thumbnail" style="width:100px">&nbsp;</th>
                                    <th class="cart-product-name">Item</th>
                                    <th class="cart-product-price" style="width:100px">Price</th>
                                    <th class="cart-product-quantity" style="width:100px">Quantity</th>
                                    <th class="cart-product-subtotal" style="width:100px">Total</th>
                                </tr>
                            </thead>
                            <tbody>
                            <perch:cartitems>
                                <tr class="cart_item">
                                    <td class="cart-product-remove text-center">
                                        <button type="submit" class="button button-3d notopmargin" name="del:<perch:cartitem id="identifier" />" value="1"><i class="icon-trash2"></i></button>
                                    </td>
                                    <td class="cart-product-thumbnail">
                                        <perch:repeater id="rptProductImages">
                                            <perch:if exists="perch_item_first"> 
                                                <perch:cartitem id="image" type="image" width="80" height="80" density="1.6" crop="true" output="tag" />
                                            </perch:if>
                                        </perch:repeater>
                                        <perch:cartitem id="image" type="image" width="80" height="80" density="1.6" crop="true" output="tag" />
                                    </td>
                                    <td class="cart-product-name">
                                        <h5 class="mb-0"><perch:cartitem id="title" /></h5>
                                        <p><i><perch:cartitem id="variant_desc" /></i></p>
                                        <div class="desc">
                                            <perch:cartitem id="description" type="textarea" markdown="true" />
                                        </div>
                                    </td>
                                    <td class="cart-product-price">
                                        <perch:cartitem id="price_without_tax" />
                                    </td>
                                    <td class="cart-product-quantity">
                                        <perch:input id="qty:<perch:cartitem id="identifier" />" class="form-control" value="<perch:cartitem id="quantity" />" type="number" min="0"  />
                                    </td>
                                    <td class="cart-product-subtotal">
                                        <span class="amount"><perch:cartitem id="total_without_tax_formatted" /></span>
                                    </td>
                                </tr>
                                </perch:cartitems>
                                <tr class="cart_item">
                                    <td colspan="6">
                                        <div class="row clearfix">
                                            <div class="col-lg-4 col-4 nopadding">
                                                <div class="row">
                                                    <div class="col-lg-8 col-7">
                                                        <perch:input type="text" value="" class="sm-form-control" placeholder="Enter Coupon Code.." id="discount_code" />
                                                    </div>
                                                    <div class="col-lg-4 col-5">
                                                        <perch:input type="submit" value="Apply Coupon" class="button button-3d button-black nomargin"/>
                                                    </div>
                                                </div>
                                            </div>
                                            <div class="col-lg-8 col-8 nopadding">
                                                <perch:input type="submit" value="Update Cart" class="button button-3d nomargin fright"/>
                                                <a href="checkout" class="button button-3d notopmargin fright">Checkout now</a>
                                            </div>
                                        </div>
                                    </td>
                                </tr>
                            </tbody>
                        </table>
                    </div>
                    <div class="row clearfix">
                        <div class="col-lg-6 clearfix"></div>
                        <div class="col-lg-6 clearfix">
                            <h4>Cart Totals</h4>
                            <div class="table-responsive">
                                <table class="table cart">
                                    <tbody>
                                        <perch:if id="total_discounts" match="gt" value="0.00">
                                        <tr class="cart_item">
                                            <th colspan="5">
                                                <strong>Discount (<perch:shop id="discount_code" />)</strong>
                                            </th>
                                            <td class="cart-product-name">
                                                <span class="amount"><perch:shop id="total_discounts_formatted" /></span>
                                            </td>
                                        </tr>
                                        <tr class="cart_item">
                                            <th colspan="5">
                                                <strong>Cart Subtotal</strong>
                                            </th>
                                            <td class="cart-product-name">
                                                <span class="amount"><perch:shop id="total_items_discounted_formatted" /></span>
                                            </td>
                                        </tr>
                                        <perch:else />
                                        <tr class="cart_item">
                                            <th colspan="5">
                                                <span class="amount"><strong>Cart Subtotal</strong></span>
                                            </th>
                                            <td class="cart-product-name">
                                                <span class="amount"><perch:shop id="total_items_formatted" /></span>
                                            </td>
                                        </tr>
                                        </perch:if>
                                        <tr class="cart_item">
                                            <th colspan="5">
                                                <strong>Shipping</strong>
                                            </th>
                                            <td class="cart-product-name">
                                                <perch:error for="all" type="login">
                                                    <p class="error">Sorry, there was a problem.</p>
                                                </perch:error>
                                                <div>
                                                    <perch:input type="select" options="<perch:shop id="shippings_list" />" class="selectpicker" id="shipping" required="true" placeholder="Please choose"  />
                                                    <perch:error for="shipping" type="required">Required</perch:error>
                                                    <perch:input type="submit" id="submit" value="OK!" class="button button-3d notopmargin fright"/>
                                                    <perch:input type="hidden" id="r" />
                                                </div>
                                            </td>
                                        </tr>
                                        <tr class="cart_item">
                                            <th colspan="5">
                                                <strong>Tax</strong>
                                            </th>
                                            <td class="cart-product-name">
                                                <span class="amount"><perch:shop id="total_tax_formatted" /></span>
                                            </td>
                                        </tr>
                                        <tr class="cart_item">
                                            <th colspan="5">
                                                <strong>Total</strong>
                                            </th>
                                            <td class="cart-product-name">
                                                <span class="amount color lead"><strong><perch:shop id="grand_total_formatted" /></strong></span>
                                            </td>
                                        </tr>
                                    </tbody>
                                </table>
                            </div>
                        </div>
                    </div>
               </perch:form>   
            <perch:else />
                <div class="style-msg errormsg">
                    <div class="sb-msg"><i class="icon-remove"></i><strong>Oh snap!</strong> Your cart is empty.</div>
                </div>
            </perch:if>         
        </div>
    </div>
</section>                        

I have not altered the code on the page, so the code above for the page is still the same.

That works if I add it to my page, but I want to have the shipping method options within my template. I'm not sure how to accomplish this? My first attempt was to use a template include, that didn't work.

Well, I found a workaround that I'm happy with. I added the perch_shop_shipping_method_form(), and changed the "method_form.html" template to just use it as a modal.

"method_form.html"

<div class="modal fade ShippingModal" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel" aria-hidden="true">
    <div class="modal-dialog modal-lg">
        <div class="modal-body">
            <div class="modal-content">
                <div class="modal-header">
                    <h4 class="modal-title" id="myModalLabel">Shipping Options</h4>
                    <button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button>
                </div>
                <div class="modal-body">
                    <perch:form id="shipping_method" method="post" app="perch_shop">
                        <perch:error for="all" type="login">
                            <p class="error">Sorry, there was a problem.</p>
                        </perch:error>

                        <div>
                            <perch:label for="shipping">Method</perch:label>
                            <perch:input type="select" options="<perch:shop id="shippings_list" />" id="shipping" required="true" placeholder="Please choose"  />
                            <perch:error for="shipping" type="required">Required</perch:error>
                        </div>
                        <div>
                            <perch:input type="submit" id="submit" value="OK!" />
                            <perch:input type="hidden" id="r" />
                        </div>
                    </perch:form>
                </div>
            </div>
        </div>
    </div>
</div>