Issue with my menu when using the plugin UberMenu

I tried to configure UberMenu with my website and it is not displaying properly. I tried it's manual integration settings, and it did not install the menu properly. It replaced all my tabs with one tab that said menu, and nothing happened upon clicking it. I tried the manual integration settings as detailed here but could not find the proper place to insert the code even with the help of Kasia on the livechat.

My theme supports two Menu locations (above and below header), and has a separate navigation-menu.php file outside of the header.php file. I have listed the code for both files here:

header.php:

<?php
/**
 * Core header file, invoked by the get_header() function
 *
 * @package Suffusion
 * @subpackage Templates
 */
global $suffusion_unified_options, $suffusion_interactive_text_fields, $suffusion_translatable_fields, $suffusion_skin_dependence, $suf_color_scheme;

if (function_exists('icl_t')) {
	foreach ($suffusion_unified_options as $id => $value) {
		/**
		 * Some strings are set interactively in the admin screens of Suffusion. If you have WPML installed, then there may be translations of such strings.
		 * This code ensures that such translations are picked up, then the unified options array is rewritten so that subsequent calls can pick it up.
		 */
		if (function_exists('icl_t') && in_array($id, $suffusion_translatable_fields) && isset($suffusion_interactive_text_fields[$id])) {
			$value = wpml_t('suffusion-interactive', $suffusion_interactive_text_fields[$id].&quot;|&quot;.$id, $value);
		}
		global $$id;
		$$id = $value;
		$suffusion_unified_options[$id] = $value;
	}
}
?>
<!DOCTYPE html>
<!--[if IE 6]> <html id=&quot;ie6&quot; <?php language_attributes(); ?>> <![endif]-->
<!--[if IE 7]> <html id=&quot;ie7&quot; <?php language_attributes(); ?>> <![endif]-->
<!--[if IE 8]> <html id=&quot;ie8&quot; <?php language_attributes(); ?>> <![endif]-->
<!--[if !(IE 6) | !(IE 7) | !(IE 8)]><!--> <html <?php language_attributes(); ?>> <!--<![endif]-->

<head>
	<meta charset=&quot;<?php bloginfo('charset'); ?>&quot; />
	<link rel=&quot;pingback&quot; href=&quot;<?php bloginfo('pingback_url'); ?>&quot; />

<?php
	suffusion_document_header();
	if (is_singular()) {
		wp_enqueue_script('comment-reply');
	}
?>
	<!--[if lt IE 9]>
	<script src=&quot;<?php echo get_template_directory_uri(); ?>/scripts/html5.js&quot; type=&quot;text/javascript&quot;></script>
	<![endif]-->
<?php
	global $suf_cpt_layouts, $suffusion_cpt_layouts;
	if (isset($suf_cpt_layouts)) {
		$suffusion_cpt_layouts = suffusion_get_associative_array($suf_cpt_layouts);
	}

	wp_head();
?>

</head>

<body <?php body_class(); ?>>
    <?php suffusion_before_page(); ?>
		<?php
			suffusion_before_begin_wrapper();
		?>
		<div id=&quot;wrapper&quot; class=&quot;fix&quot;>
		<?php
			suffusion_after_begin_wrapper();
		?>
			<div id=&quot;container&quot; class=&quot;fix&quot;>
				<?php
					suffusion_after_begin_container();
				?>

navigation-menu.php:

<?php
/**
 * Builds a navigation menu for the theme. It makes use of the options defined in the &quot;Other Graphical Elements&quot; section and can be used for either menu location.
 * Users can override this in a child theme. Note that if you want to have different menus for the Top and the Main Navigation bars, you can create files called
 * navigation-menu-top.php and navigation-menu-main.php respectively. If either file doesn't exist, this file will be picked.
 *
 * @since 3.8.3
 * @package Suffusion
 * @subpackage Custom
 */

global $suffusion_menu_location, $suffusion_page_option, $suffusion_cats_option, $suffusion_links_option, $suffusion_menus_option, $suffusion_echo_menu;

global $suf_nav_pages_style, $suf_nav_page_tab_title, $suf_nav_page_tab_link, $suf_navt_pages_style, $suf_navt_page_tab_title, $suf_navt_page_tab_link;
global $suf_nav_cat_style, $suf_nav_cat_tab_title, $suf_nav_cat_tab_link, $suf_navt_cat_style, $suf_navt_cat_tab_title, $suf_navt_cat_tab_link;
global $suf_nav_links_style, $suf_nav_links_tab_title, $suf_nav_links_tab_link, $suf_navt_links_style, $suf_navt_links_tab_title, $suf_navt_links_tab_link;
global $suf_nav_entity_order, $suf_navt_entity_order, $suf_nav_pages_all_sel, $suf_nav_cats_all_sel, $suf_nav_links_all_sel, $suf_navt_pages_all_sel, $suf_navt_cats_all_sel, $suf_navt_links_all_sel;
global $suf_nav_menus_all_sel, $suf_navt_menus_all_sel;

switch ($suffusion_menu_location) {
	case 'top':
		$pages_style = $suf_navt_pages_style;
		$page_tab_title = stripslashes($suf_navt_page_tab_title);
		$page_tab_link = $suf_navt_page_tab_link;
		$page_all_sel = $suf_navt_pages_all_sel;
		$cat_style = $suf_navt_cat_style;
		$cat_tab_title = stripslashes($suf_navt_cat_tab_title);
		$cat_tab_link = $suf_navt_cat_tab_link;
		$cat_all_sel = $suf_navt_cats_all_sel;
		$links_style = $suf_navt_links_style;
		$links_tab_title = stripslashes($suf_navt_links_tab_title);
		$links_tab_link = $suf_navt_links_tab_link;
		$link_all_sel = $suf_navt_links_all_sel;
		$menus_all_sel = $suf_navt_menus_all_sel;
		$entity_order = $suf_navt_entity_order;
		break;
	default:
		$pages_style = $suf_nav_pages_style;
		$page_tab_title = stripslashes($suf_nav_page_tab_title);
		$page_tab_link = $suf_nav_page_tab_link;
		$page_all_sel = $suf_nav_pages_all_sel;
		$cat_style = $suf_nav_cat_style;
		$cat_tab_title = stripslashes($suf_nav_cat_tab_title);
		$cat_tab_link = $suf_nav_cat_tab_link;
		$cat_all_sel = $suf_nav_cats_all_sel;
		$links_style = $suf_nav_links_style;
		$links_tab_title = stripslashes($suf_nav_links_tab_title);
		$links_tab_link = $suf_nav_links_tab_link;
		$link_all_sel = $suf_nav_links_all_sel;
		$menus_all_sel = $suf_nav_menus_all_sel;
		$entity_order = $suf_nav_entity_order;
		break;
}
global $$suffusion_page_option, $$suffusion_cats_option, $$suffusion_links_option, $$suffusion_menus_option;

$selected_menus = $$suffusion_menus_option;
$menu_args = array(
	'sort_column' => 'menu_order'
);

if ($menus_all_sel == 'selected') {
	if (trim($selected_menus) == '') {
		$menus_included = array();
	}
	else {
		$menus_included = explode(',', $selected_menus);
	}
}

$menu_locations = get_nav_menu_locations();

if (isset($menus_included) && isset($menu_locations[$suffusion_menu_location])) {
	$menu_in_location = $menu_locations[$suffusion_menu_location];
	if (!in_array($menu_in_location, $menus_included)) {
		$menus_included[] = $menu_in_location;
	}
}

if (isset($menus_included)) {
	if (count($menus_included) == 0) {
		$menus_to_show = array();
	}
	else {
		$menu_args['include'] = $menus_included;
		$menus_to_show = wp_get_nav_menus($menu_args);
	}
}
else {
	$menus_to_show = wp_get_nav_menus($menu_args);
}

$entity_order = suffusion_get_entity_order($entity_order, 'nav');
$entity_order = explode(',', $entity_order);
$home_link = suffusion_get_home_link_html($suffusion_menu_location);
$ret_str = $home_link;
foreach ($entity_order as $entity) {
	if ($entity == 'pages') {
		$selected_pages = $$suffusion_page_option;
		$page_args = array(
			'sort_column' => 'menu_order,post_title',
			'child_of' => 0,
			'echo' => 0,
			'suffusion_nav_display' => $pages_style,
		);

		if ($page_all_sel == 'selected') {
			if (trim($selected_pages) == '') {
				$page_args = array();
			}
			else {
				$page_args['include'] = $selected_pages;
			}
		}
		else if ($page_all_sel == 'exclude-selected') {
			$page_args['exclude'] = $selected_pages;
		}
		else if ($page_all_sel == 'exclude-all') {
			$page_args = array();
		}

		if ($pages_style == 'rolled-up' && count($page_args) != 0) {
			$page_args['title_li'] = &quot;<a href='&quot; . ($page_tab_link == '' ? '#'
					: $page_tab_link) . &quot;'>&quot; . $page_tab_title . &quot;</a>&quot;;
		}
		else if ($pages_style == 'flattened' && count($page_args) != 0) {
			$page_args['title_li'] = '';
		}
		if (count($page_args) == 0) {
			$page_str = '';
		}
		else {
			$page_str = wp_list_pages($page_args);
		}
		$ret_str .= $page_str;
	}
	else if ($entity == 'categories') {
		$cat_args = array(
			'orderby' => 'name',
			'order' => 'ASC',
			'child_of' => 0,
			'echo' => 0,
			'current_category' => 0,
		);

		if (function_exists('mycategoryorder')) {
			$cat_args['orderby'] = 'order';
		}

		$selected_cats = $$suffusion_cats_option;
		if ($cat_all_sel == 'selected') {
			if (trim($selected_cats) == '') {
				$cat_args = array();
			}
			else {
				$cat_args['include'] = $selected_cats;
			}
		}
		else if ($cat_all_sel == 'exclude-selected') {
			$cat_args['exclude'] = $selected_cats;
		}
		else if ($cat_all_sel == 'exclude-all') {
			$cat_args = array();
		}

		if ($cat_style == 'rolled-up' && count($cat_args) != 0) {
			$cat_args['title_li'] = &quot;<a href='&quot; . ($cat_tab_link == '' ? '#'
					: $cat_tab_link) . &quot;'>&quot; . $cat_tab_title . &quot;</a>&quot;;
		}
		else if ($cat_style == 'flattened' && count($cat_args) != 0) {
			$cat_args['title_li'] = '';
		}

		if (count($cat_args) == 0) {
			$cat_str = '';
		}
		else {
			$cat_str = wp_list_categories($cat_args);
		}
		$ret_str .= $cat_str;
	}
	else if ($entity == 'links') {
		$link_args = array(
			'orderby' => 'name',
			'order' => 'ASC',
			'limit' => -1,
			'echo' => 0,
			'categorize' => 0,
			'title_before' => '',
			'title_after' => '',
		);
		if (function_exists('mylinkorder')) {
			$link_args['orderby'] = 'order';
		}

		$selected_links = $$suffusion_links_option;
		if ($link_all_sel == 'selected') {
			if (trim($selected_links) == '') {
				$link_args = array();
			}
			else {
				$link_args['include'] = $selected_links;
			}
		}
		else if ($link_all_sel == 'exclude-selected') {
			$link_args['exclude'] = $selected_links;
		}
		else if ($link_all_sel == 'exclude-all') {
			$link_args = array();
		}

		if ($links_style == 'rolled-up' && count($link_args) != 0) {
			$link_args['title_li'] = &quot;<a href='&quot; . ($links_tab_link == '' ? '#'
					: $links_tab_link) . &quot;'>&quot; . $links_tab_title . &quot;</a>&quot;;
		}
		else if ($links_style == 'flattened' && count($link_args) != 0) {
			$link_args['title_li'] = '';
		}

		if (count($link_args) == 0) {
			$link_str = '';
		}
		else {
			$link_str = wp_list_bookmarks($link_args);
		}
		$ret_str .= $link_str;
	}
	else if ((strlen($entity) >= 5 && substr($entity, 0, 5) == 'menu-')) {
		if (count($menus_to_show) != 0) {
			$menu_print_args = array(
				'container' => '',
				'menu_class' => 'menu',
				'echo' => false,
				'depth' => 0,
				'theme_location' => $suffusion_menu_location,
				'items_wrap' => '%3$s',
			);
			if (current_theme_supports('mega-menus')) {
				$menu_print_args['walker'] = new Suffusion_MM_Walker();
			}
			$menu_str = '';
			$menu_entity_id = (int)substr($entity, 5);
			foreach ($menus_to_show as $menu) {
				if ($menu->term_id != $menu_entity_id) continue;
				$menu_print_args['menu'] = $menu->term_id;
				$this_menu_str = wp_nav_menu($menu_print_args);
				$this_menu_str = preg_replace('/^<ul id=&quot;[-a-zA-Z0-9]*&quot; class=&quot;menu&quot;>/', '', $this_menu_str);
				$this_menu_str = preg_replace('/<\/ul>$/', '', $this_menu_str);
				$menu_str .= $this_menu_str;
			}
			$ret_str .= $menu_str;
		}
	}
}
if (trim($ret_str) != '') {
	$ret_str = &quot;<ul class='sf-menu'>\n&quot; . $ret_str . &quot;\n</ul>\n&quot;;
}

if ($suffusion_echo_menu) {
	echo $ret_str;
}
?>

I have enabled access to my site for anyone who needs it. I have scoured other forums to find solutions and have not found anything that has worked. Please help me to get this menu installed as my site looks hideous without it.