Custom Post Paging (Page Navigation)

I’m going insane. I’m busy writing my first plugin and using custom post types. I have basically gotten everything to work except for the page navigation. I have read everything that I could find but I still haven’t gotten it to work.

I use a shortcode to display the post content and I got paging to work on that but when I set the page as the landing page navigation doesn’t word. The page only refreshes with the same info.

Here is how the custom post type is registered:

/* Set up the post types */
add_action( 'init', 'exc_agriq_equipment_register_post_types' );

/* Registers the post type */
function exc_agriq_equipment_register_post_types() {
	register_post_type( 'exc_agriq_equipment',
		array(
			'labels' => array(
				'name' => __( 'Equipment' ),
				'singular_name' => __( 'Equipment' ),
				'add_new' => __( 'Add New Equipment' ),
				'add_new_item' => __( 'Add New Equipment' ),
				'edit' => __( 'Edit' ),
				'edit_item' => __( 'Edit Equipment' ),
				'new_item' => __( 'New Equipment' ),
				'view' => __( 'View Equipment' ),
				'view_item' => __( 'View Equipment' ),
				'search_items' => __( 'Search Equipment' ),
				'not_found' => __( 'No Equipment found' ),
				'not_found_in_trash' => __( 'No Equipment found in Trash' ),
			),
			'public' => true,
			'show_in_nav_menus' => false,
			'show_ui' => true,
			'publicly_queryable' => true,
			'exclude_from_search' => false,
			'hierarchical' => false,
			'capability_type' => 'post',
			'query_var' => true,
			//'rewrite' => false,
			'has_archive' => true,
			'supports' => array('title', 'editor'),
			'rewrite' => array( 'slug' => 'exc', 'with_front' => true),
		)
	);
}

This is the shortcode

<?php
//Add thickbox files
function add_themescript(){
		$agriquip_plugin_url = plugins_url('agriquip', '__FILE__');
    wp_enqueue_script('jquery');
    wp_enqueue_script('thickbox',null,array('jquery'));
    wp_enqueue_style('thickbox.css', '/'.WPINC.'/js/thickbox/thickbox.css', null, '1.0');
	wp_enqueue_script('exc-equal-heights', $agriquip_plugin_url. '/js/equal-heights.js',array('jquery'));
}

add_action('init','add_themescript');

//Add css files
add_action('wp_head', 'agriquip_style' );

function agriquip_style()
  {
  $agriquip_plugin_url = plugins_url('agriquip', '__FILE__');
  echo '<link rel="stylesheet" href="'.$agriquip_plugin_url.'/css/agriquip.css" type="text/css" />';
  }

//Register equipment shortcode
add_shortcode( 'equipment', 'exc_agriq_equipment_shortcode' );

//The callback function that will replace [equipment]
function exc_agriq_equipment_shortcode() {
?>
<script type="text/javascript">
jQuery(document).ready(

	function() {
		//Equal columns
    jQuery(".equalHeights").equalHeights();
    }
);

</script>
<?php
 echo "<ul class='equalHeights'>";
    $paged = (get_query_var('paged')) ? get_query_var('paged') : 1;
    $loop = new WP_Query( array(
      'post_type' => 'exc_agriq_equipment',
      'posts_per_page' => 16,
      'paged'=>$paged,
    )
		);
	//$loop = new WP_Query( array( 'post_type' => 'exc_agriq_equipment', 'posts_per_page' => 16, 'paged' => $paged ) );

        while ( $loop->have_posts() ) : $loop->the_post(); 

				$exc_agriq_year = get_post_meta( get_the_ID(), 'exc_agriq_equipment_year', true );
				$exc_agriq_hours = get_post_meta( get_the_ID(), 'exc_agriq_equipment_hours', true );
				$exc_agriq_price = get_post_meta( get_the_ID(), 'exc_agriq_equipment_price', true );
				$exc_agriq_kw = get_the_term_list( get_the_ID(), 'exc_equipment_kw', '', ', ', '');

				?>
				<li class="agriq-equipment-container">
					<div class="agriq-equipment-detail">
						<?php
						$images = get_post_meta(get_the_ID(), 'exc_agriq_equipment_images', false);
						$excagriqID = get_the_ID();

						echo "<div class='agrig-equipment-images'>";
            foreach ($images as $att) {
              // get image's source based on size, can be 'thumbnail', 'medium', 'large', 'full' or registed post thumbnails sizes
              $srcthumb = wp_get_attachment_image_src($att, 'thumbnail');
              $srcthumb = $srcthumb[0];
							$src = wp_get_attachment_image_src($att, 'full');
              $src = $src[0];

              // show image
              echo "<div class='agriq-equipment-image'><a href='$src' class='thickbox' rel='". $excagriqID ."'><img src='$srcthumb' width='150px' height='150px'/></a></div>";
						}
						?>
						</div>
						<div class="agriq-equipment-title"><h4><?php echo the_title(); ?></h4></div>
						<div class="agriq-equipment-description"><?php echo the_content(); ?></div>
						<div class="agriq-equipment-kw"><span>Kw:</span> <?php echo $exc_agriq_kw; ?></div>
						<div class="agriq-equipment-year"><span>Jaar:</span> <?php echo $exc_agriq_year; ?></div>
						<div class="agriq-equipment-hours"><span>Ure:</span> <?php echo $exc_agriq_hours; ?></div>
						<div class="agriq-equipment-price"><span>Prys:</span> R<?php echo $exc_agriq_price; ?> BTW Ingesluit</div>
					</div>
				</li>

				<?php
        endwhile;
				echo "</ul>";
				if (function_exists("pagination")) {
    pagination($loop->max_num_pages);
		}
}

?>

As soon I get this sorted I can start with the paging for the taxonomies.

Help would be greatly appreciated