href instead of link_path should be used when building the mega menu

href is returned in the array from the menu_tree_all_data call. After a few attempts I realized that both the menu_tree_page_data and menu_tree_all_data needed to be utilized to get the result we were after. We were losing the active trail. For some reason the menu_tree_all_data does not have the active trail set properly. We came with a solution if you are interested?

We modified _megamenu_get_menu_tree to return more data with the following changes

/**
 * Retrieve a menu and pre-style before theming
 *
 * This function currently removes all "hidden" items, which could be
 * handled in the single iteration of the theme function.  But, I forsee
 * a need for other prep work that might be simmplfied with this second function
 *
 * Will be used in the future to add/alter attributes prior to theming
 *
 * @param $menuname
 *    The name of the menu to extract
 *
 * @return
 *    The pre-styled menu tree
 */
function _megamenu_get_menu_tree($menuname) {
  $menutree = menu_tree_all_data($menuname);
  $menutree_page = menu_tree_page_data($menuname);
  
  foreach($menutree_page as $level1_key => $level1_item) {
		if ($level1_item['link']['in_active_trail']) {
			$menutree[$level1_key]['link']['in_active_trail'] = TRUE;
		}
		if ($link1_item['link']['hidden'] == 1) {
      unset($menutree[$link1_key]);
    }
    else {
			if ($level1_item['below']) {
				foreach($level1_item['below'] as $level2_key => $level2_item) {
					if ($level2_item['link']['in_active_trail']) {
						$menutree[$level1_key]['below'][$level2_key]['link']['in_active_trail'] = TRUE;
					}
					
					if ($level2_item['link']['hidden'] == 1) {
	        	unset($menutree[$level1_key]['below'][$level2_key]);
	        }
					else {
						if ($level2_item['below']) {
							foreach($level2_item['below'] as $level3_key => $level3_item) {
								if ($level3_item['link']['in_active_trail']) {
									$menutree[$level1_key]['below'][$level2_key]['below'][$level3_key]['link']['in_active_trail'] = TRUE;
								}
								
								if ($level3_item['link']['hidden'] ==1) {
		                unset($menutree[$level1_key]['below'][$level2_key]['below'][$level3_key]);
		            }
		            else if ($level3_item['below']){
                	unset($menutree[$level1_key]['below'][$level2_key]['below'][$level3_key]['below']);
            		}	
							} // end level 3 loop
						}
					}
				} // end level 2 loop
			}
		}
  } // end level 1 loop
  return $menutree;
}

We also updated your megamenu theme function to utilize drupals themable item list

/**
 * Theme a menu tree
 * 
 * This function takes a menu tree, such as primary links, and generates 
 * HTML markup of the menu so that it can be styled as a mega menu. It
 * takes the first three nested levels of the menu tree and creates a
 * structure of nested lists with appropriate classes and IDs assigned (even,
 * odd, active, etc.).
 *
 * First, we iterate through the first level of menu items (branch/tier-1/megamenu-bin). Each
 * item will be the megamenu-parent of the second level of links (twig/tier-2/megamenu-slot).
 * Next we iterate through the twigs of the menu tree to fill the megamenu-bins. A bin
 * is an unordered list which contains slots (twig/tier-2 items). To fill the slots we iterate
 * through each twig, where the leaves are the deepest level of the menu tree (tier-3). Each leaf
 * is a list item containing a tier-3 menu link.
 *
 * Abbreviations: t1, t2, & t3 stands for tier-1, tier-2, and tier-3
 * respectively. They represent nested level menu items.
 *
 * @param $menutree
 *    The menu tree to be marked up (i.e. primary_links)
 * @return
 *    HTML markup for a mega menu
 *
 */
function megamenu_theme_menu_tree($menu_name) {
  $menutree = _megamenu_get_menu_tree($menu_name);

  $skin = _megamenu_get_skin_by_name($menu_name);
  $menu_orientation = _megamenu_get_menu_orientation_by_name($menu_name);

  // TODO: Currently, these attributes are set menu wide. Eventually these might should be set per menu level?
  $slot_orientation = _megamenu_get_slot_orientation_by_name($menu_name); /* TODO: temp value, should be attached to branch level in admin interface */
  $slot_attributes = _megamenu_get_slot_attributes_by_name($menu_name); /* TODO: temp value, should be attached to twig level in admin interface. */


  $t1_position = 0;
  $branch_count = count($menutree);
  
  foreach ($menutree as $branch) {
  
    if ($branch['below']){
    
      $t2_position = 0;
      $twig_count = count($branch['below']);
      
      foreach ($branch['below'] as $twig) {
    		
        if ($twig['below']){
        
          $t3_position = 0;
          $leaf_count = count($twig['below']);
          foreach ($twig['below'] as $leaf) {
          
		    		// are we active / active-trail ?
		    		$active = _megamenu_active_classes($leaf);
				    $leaf_link_options['attributes'] = array('class'=>$active);
          	
            $t3_count_attributes = _megamenu_count_attributes($t3_position, $leaf_count);
            $t3_position++;
          	
          	$leaf_items[] = array(
          		'id'		=> 'megamenu-mlid-'.$leaf['link']['mlid'],
          		'class'	=> 'megamenu-item'.$t3_count_attributes.$active,
          		'data'	=> l($leaf['link']['link_title'], $leaf['link']['href'], $leaf_link_options)
          	);
          	
          } // END leaf iteration
          
          // Build leaf list
          $leaf_list_options = array(
          	'class'=> 'megamenu-items '.$slotattributes
          );
          $leaf_items_list = theme('item_list',$leaf_items, NULL, 'ul',$leaf_list_options);
          $leaf_items_list = _megamenu_strip_list_wrapper($leaf_items_list);
          unset($leaf_items);
          
        } // END leaf detection
        
        $t2_count_attributes = _megamenu_count_attributes($t2_position, $twig_count);
        $t2_position++;

    		// are we active / active-trail ?
    		$active = _megamenu_active_classes($twig);
				$link_options['attributes'] = array('class'=>$active);
				
				// This twig's <li> content
				$twig_data = '<h3 class="megamenu-slot-title">';
				$twig_data .= l($twig['link']['link_title'], $twig['link']['href'], $link_options);
				$twig_data .= '</h3>';
				$twig_data .= $leaf_items_list;
				
				$twig_items[] =	array(
					'id'		=> 'megamenu-mlid-'.$twig['link']['mlid'],
					'class' => 'megamenu-slot '.$t2_count_attributes.$active,
					'data'	=> $twig_data
				);
				unset($leaf_items_list);
      } // END twig iteration

      // Build twig list
      $twig_list_options = array(
      	'class' => 'megamenu-bin megamenu-slots-'.$slot_orientation
      );
      $twig_items_list = theme('item_list', $twig_items, NULL, 'ul', $twig_list_options);
      $twig_items_list = _megamenu_strip_list_wrapper($twig_items_list);
      unset($twig_items);
      
    }  // END twig detection
	

	  // setup active link classes
  	$active = _megamenu_active_classes($branch);
  	
  	// Link options
		$branch_link_options['attributes'] = array('class'=>$active);
		
  	// setup $t1_count_attributes (classes)
  	$t1_count_attributes = _megamenu_count_attributes($t1_position, $branch_count);
	  $t1_position++;  
  
    $branch_items[] = array(
    	'id' => 'megamenu-mlid-'.$branch['link']['mlid'],
    	'class' => 'megamenu-parent'.$t1_count_attributes.' menu-'.$branch['link']['mlid'].$active,
    	'data' =>  '<h2 class="megamenu-parent-title">'.l($branch['link']['link_title'], $branch['link']['href'], $branch_link_options).'</h2>'.$twig_items_list
    );
    unset($twig_items_list);

  } // END branch iteration
  
  // Build branch list
  $branch_list_options = array(
  	'id' 		=> 'megamenu-'.$menu_name,
  	'class' => 'megamenu-menu '.$menu_orientation .' megamenu-skin-'.$skin
  );
		
  $output = theme('item_list', $branch_items, NULL, 'ul', $branch_list_options);
  $output = _megamenu_strip_list_wrapper($output);
  unset($branch_items);
  
  return $output;
}

I believe my partner in crime electblake reached out to you already about being co-maintainers. Are you interested?

Sorry about that. There was a duplicate function that ended up getting copied by mistake.

New patch attached

*** Edit ***
Sorry patch is incorrect. It was patched from the previous patch and not from the current version. I will upload a new patch

This should do it.