Used code I found on css tricks to remove the li tags from wp_nav_menu.
$menu_parameters = array( 'container' => false, 'echo' => false, 'items_wrap' => '%3$s', 'depth' => 0, ); <?php echo strip_tags(wp_nav_menu( $menu_parameters ), '<a>' ); ?>
I placed $menu_parameters in functions.php and called it in my index file and everything was working great until I separated my index files into their appropriate php files. After I moved the strip_tag function into the header.php and then called it using get_header, the nav now falls back to the wp default. Any ideas?