WordPress Section Index w/ shortcode and many options

gistfile1.php

			<?php $the_content = apply_filters('the_content', $post->post_content);
			$the_content = explode("<p>[MENU]</p>",$the_content); ?>
			<?= $the_content[0]; ?>
			
			<?php
				/* GET CUSTOM FIELDS */
				$menu_type = get_post_meta($post->ID, 'menu_type', true);
				$menu_page_curl = get_post_meta($post->ID, 'menu_page_curl', true);
				$menu_custom_array = get_post_meta($post->ID, 'menu_custom_array', true);
				$menu_more_text = get_post_meta($post->ID, 'menu_more_text', true);
				$menu_more_id = get_post_meta($post->ID, 'menu_more_id', true);
				/* SET TYPE CONDITONALS */
				if($menu_type=='' || $menu_type=='Default' || $menu_type=='Square') {
					$menu_type_class = ' square';
					$menu_columns_class = ' three-cols';
					$menu_thumb_type = 'square-thumb';
					$menu_fallback_width = 210;
					$menu_fallback_height = 210;
				}
				elseif($menu_type=='Polaroid') {
					$menu_type_class = ' polaroid';
					$menu_columns_class = ' three-cols';
					$menu_thumb_type = 'polaroid-thumb';
					$menu_fallback_width = 188;
					$menu_fallback_height = 146;
				}
				elseif($menu_type=='Letterbox (White)') {
					$menu_type_class = ' letterbox';
					$menu_columns_class = ' two-cols';
					$menu_thumb_type = 'letterbox-thumb';
					$menu_fallback_width = 80;
					$menu_fallback_height = 80;
				}
				elseif($menu_type=='Letterbox (Green)') {
					$menu_type_class = ' letterbox related';
					$menu_columns_class = ' two-cols';
					$menu_thumb_type = 'letterbox-thumb';
					$menu_fallback_width = 80;
					$menu_fallback_height = 80;
				}
			?>	
			<?php global $pages_array; ?>
			<?php $menu_custom_array ? $pages_array = explode(",", $menu_custom_array) : $pages_array = ''
				/* IF NO CUSTOM ARRAY, SET NULL */ ?>
			<?php query_posts( array( 'post_parent' => $post->ID, 'post_type' => 'page', 'posts_per_page' => -1, 'orderby' => 'title,menu_order', 'order' => 'ASC', 'post__not_in' => $excluded_pages_array, 'post__in' => $pages_array ) );
				/* QUERY PAGES */ ?>
			<?php if (have_posts()) : ?>
			<section class="sub-pages<?= $menu_type_class; ?><?= $menu_columns_class; ?><?= $menu_page_curl==1 ? ' curl' : '' ?>">
				<?php while (have_posts()) : the_post(); ?>
				<article>
					<a href="<?php the_permalink(); ?>">
						<h2>
							<?php the_title(); ?>
						</h2>
						 <?php if ($post->post_excerpt!==''): ?>
						<p>
							<?php the_excerpt(); ?>
						</p>
						<?php endif; ?>
						<?php if(has_post_thumbnail()):?>
						<?php the_post_thumbnail($menu_thumb_type, array('alt' => ''.get_the_title().'', 'title' => '' )); ?>
						<?php else: ?>
						<img src="/assets/images/fallback.gif" alt="<?php the_title(); ?>" width="<?= $menu_fallback_width; ?>" height="<?= $menu_fallback_height; ?>" />
						<?php endif; ?>
					</a>
				</article>
				<?php endwhile;?>
				<?php if($menu_more_text && $menu_more_id): ?>
				<p class="more">
					<a href="<?= get_page_link($menu_more_id); ?>">
						<?= $menu_more_text; ?>
					</a>
				</p>
				<?php endif; ?>
			</section>
			<?php endif; ?>
			<?php wp_reset_query();?>
			
			<?= $the_content[1]; ?>