This plugin breaks the WP admin bar.

I fixed your plugin. You’ll see my edits below:

class MasterSharedMenu {
	protected $loader;
	protected $plugin_name;
	protected $version;
	protected $current_blog_id; //Brad's hack

	public function __construct() {
		$this->plugin_name = 'multisitesharedmenu';
		$this->version = '1.2';
		$this->current_blog_id = get_current_blog_id(); //Brad's hack

		$this->define_admin_hooks();
		$this->define_public_hooks();
	}

	private function define_admin_hooks() {
		$this->add_mfs_menu();
	}

	private function define_public_hooks() {
		add_filter( 'pre_wp_nav_menu' , array( $this, 'menuswitch_check'), 10, 2 );
		add_filter( 'show_admin_bar', array( $this, 'check_restore_blog_menu' ) ); //Brad's hack
	}

	// Checks if options set to switch menu. If so, switch to the appropriate site and change the menu to load the desired menu....
	public function menuswitch_check( $a, $menu_object ) {
		if( !( $mfsSettings = $this->validate_mfs_set() )) {
			return false;
		}

		$navigation_affected = $mfsSettings['destinationMenuLocation'];

		if( !is_array( $navigation_affected ) ) {
			$navigation_affected = array( $navigation_affected ); // backwards-compatibility
		} 

		// nav menus now stored as an array, loop through each item
		foreach ( $navigation_affected as $menu) {
			if (isset( $menu_object )) {
				if( $menu == $menu_object->theme_location ) {
					$switchSite = get_blog_details($mfsSettings['sourceSiteID']);
					switch_to_blog($switchSite->blog_id);
				}
			}
		}
		return;
	}

	// Switch back to the current blog/site if plugin settings were used.
	public function check_restore_blog_menu() {//Brad's hack
		switch_to_blog($this->current_blog_id); //Brad's hack
		return true;//Brad's hack
	}

I had to make some more changes and forgot to update, here you go:

<?php
// allow this plugin to access functions from WP core before they would normally be avalible
require_once( ABSPATH . 'wp-includes/pluggable.php' ); //Brad's hack

class MasterSharedMenu {
	protected $loader;
	protected $plugin_name;
	protected $version;
	protected $current_blog_id; //Brad's hack

	public function __construct() {
		$this->plugin_name = 'multisitesharedmenu';
		$this->version = '1.2';
		$this->current_blog_id = get_current_blog_id(); //Brad's hack

		$this->define_admin_hooks();
		$this->define_public_hooks();
	}

	private function define_admin_hooks() {
		$this->add_mfs_menu();
	}

	private function define_public_hooks() {
		add_action( 'plugins_loaded', array( $this, 'check_if_user_logged_in' ) ); //Brad's hack

		add_filter( 'pre_wp_nav_menu' , array( $this, 'menuswitch_check'), 10, 2 );
		add_filter( 'wp_nav_menu_items', array( $this, 'check_restore_blog_menu' ), 10, 2 );
		if ( $this->check_if_user_logged_in() ) { //Brad's hack
			add_filter( 'show_admin_bar', array( $this, 'check_restore_blog_menu' ) ); //Brad's hack
		} //Brad's hack
	}

	public function check_if_user_logged_in() { //Brad's hack
		return is_user_logged_in(); //Brad's hack
	} //Brad's hack

	// Checks if options set to switch menu. If so, switch to the appropriate site and change the menu to load the desired menu....
	public function menuswitch_check( $a, $menu_object ) {
		if( ! ( $mfsSettings = $this->validate_mfs_set() ) ) {
			return false;
		}
		
		$navigation_affected = $mfsSettings['destinationMenuLocation'];
		
		if( !is_array( $navigation_affected ) ) {
			$navigation_affected = array( $navigation_affected ); // backwards-compatibility
		} 
		
		// nav menus now stored as an array, loop through each item
		foreach ( $navigation_affected as $menu ) {
			if ( isset( $menu_object ) ) {
				if( $menu == $menu_object->theme_location ) {
					$switchSite = get_blog_details( $mfsSettings['sourceSiteID'] );
					switch_to_blog( $switchSite->blog_id );
				}
			}
		}
		return;
	}
	
	// Switch back to the current blog/site if plugin settings were used.
	public function check_restore_blog_menu( $items = null, $args = null ) { //Brad's hack
		switch_to_blog( $this->current_blog_id ); //Brad's hack
		if ( null != $items ) { //Brad's hack
			return $items;
		} //Brad's hack
		else { //Brad's hack
			return true; //Brad's hack
		} //Brad's hack
	}