One thing I would say is Section D should take advantage of the Roots Bootstrap Walker and WordPress Menus. You just need to create a secondary navigation menu and change the classes when the menu is called:
<?php
if (has_nav_menu('secondary_navigation')) :
wp_nav_menu(array('theme_location' => 'secondary_navigation', 'menu_class' => 'nav nav-pills nav-stacked'));
endif;
?>