PHP issue causing router.php error in menu (SEF Link issue)...

Working on a joomla installation on a Linux server. Some nasty malicious code somehow made it onto my desktop which I normally have locked down tight. It attached itself to my ftp program, uploaded snippets of code to the joomla installation (on several domains actually). Well, I found every instance of code and can get into the back end now no problem. But when trying to access the front end of the site (which I had at the moment, put offline), I get this:

Fatal error: Call to a member function getDefault() on a non-object in /XXXX/XXXXX/public_html/XXXXXXX/includes/router.php on line 176

What is found on line 176 is:
$item = $menu->getDefault();

The Full Code of the router.php is attached in the code portion of this post.  I was wondering if it was something in my sql database as I've tried just about everything on the Joomla install...

<?php
/**
* @version		$Id: router.php 8180 2007-07-23 05:52:29Z eddieajau $
* @package		Joomla.Framework
* @subpackage	Application
* @copyright	Copyright (C) 2005 - 2008 Open Source Matters. All rights reserved.
* @license		GNU/GPL, see LICENSE.php
* Joomla! is free software. This version may have been modified pursuant
* to the GNU General Public License, and as distributed it includes or
* is derivative of works licensed under the GNU General Public License or
* other free or open source software licenses.
* See COPYRIGHT.php for copyright notices and details.
*/
 
// Check to ensure this file is within the rest of the framework
defined('JPATH_BASE') or die();
 
/**
 * Class to create and parse routes for the site application
 *
 * @package 	Joomla
 * @since		1.5
 */
class JRouterSite extends JRouter
{
	/**
	 * Class constructor
	 *
	 * @access public
	 */
	function __construct($options = array()) {
		parent::__construct($options);
	}
 
	function parse(&$uri)
	{
		$vars = array();
 
		// Get the application
		$app =& JFactory::getApplication();
 
		if($app->getCfg('force_ssl') == 2 && strtolower($uri->getScheme()) != 'https') {
			//forward to https
			$uri->setScheme('https');
			$app->redirect($uri->toString());
		}
 
 
		// Get the path
		$path = $uri->getPath();
 
		//Remove the suffix
		if($this->_mode == JROUTER_MODE_SEF)
		{
 
			if($app->getCfg('sef_suffix') && !(substr($path, -9) == 'index.php' || substr($path, -1) == '/'))
			{
				if($suffix = pathinfo($path, PATHINFO_EXTENSION))
				{
					$path = str_replace('.'.$suffix, '', $path);
					$vars['format'] = $suffix;
				}
			}
		}
 
		//Remove basepath
		$path = substr_replace($path, '', 0, strlen(JURI::base(true)));
 
		//Remove prefix
		$path = str_replace('index.php', '', $path);
 
		//Set the route
		$uri->setPath(trim($path , '/'));
 
		$vars += parent::parse($uri);
 
		return $vars;
	}
 
	function &build($url)
	{
		$uri =& parent::build($url);
 
		// Get the path data
		$route = $uri->getPath();
 
		//Add the suffix to the uri
		if($this->_mode == JROUTER_MODE_SEF && $route)
		{
			$app =& JFactory::getApplication();
 
			if($app->getCfg('sef_suffix') && !(substr($route, -9) == 'index.php' || substr($route, -1) == '/'))
			{
				if($format = $uri->getVar('format', 'html'))
				{
					$route .= '.'.$format;
					$uri->delVar('format');
				}
			}
 
			if($app->getCfg('sef_rewrite'))
			{
				//Transform the route
				$route = str_replace('index.php/', '', $route);
			}
		}
 
		//Add basepath to the uri
		$uri->setPath(JURI::base(true).'/'.$route);
 
		return $uri;
	}
 
	function _parseRawRoute(&$uri)
	{
		$vars   = array();
 
		$menu =& JSite::getMenu(true);
 
		//Handle an empty URL (special case)
		if(!$uri->getVar('Itemid') && !$uri->getVar('option'))
		{
			$item = $menu->getDefault();
			if(!is_object($item)) return $vars; // No default item set
 
			//Set the information in the request
			$vars = $item->query;
 
			//Get the itemid
			$vars['Itemid'] = $item->id;
 
			// Set the active menu item
			$menu->setActive($vars['Itemid']);
 
			return $vars;
		}
 
		//Get the variables from the uri
		$this->setVars($uri->getQuery(true));
 
		//Get the itemid, if it hasn't been set force it to null
		$this->setVar('Itemid', JRequest::getInt('Itemid', null));
 
		//Only an Itemid ? Get the full information from the itemid
		if(count($this->getVars()) == 1)
		{
			$item = $menu->getItem($this->getVar('Itemid'));
			$vars = $vars + $item->query;
		}
 
		// Set the active menu item
		$menu->setActive($this->getVar('Itemid'));
 
		return $vars;
	}
 
	function _parseSefRoute(&$uri)
	{
		$vars   = array();
 
		$menu  =& JSite::getMenu(true);
		$route = $uri->getPath();
 
		//Get the variables from the uri
		$vars = $uri->getQuery(true);
 
		//Handle an empty URL (special case)
		if(empty($route))
		{
 
			//If route is empty AND option is set in the query, assume it's non-sef url, and parse apropriately
			if(isset($vars['option']) || isset($vars['Itemid'])) {
				return $this->_parseRawRoute($uri);
			}
 
			$item = $menu->getDefault();
 
			//Set the information in the request
			$vars = $item->query;
 
			//Get the itemid
			$vars['Itemid'] = $item->id;
 
			// Set the active menu item
			$menu->setActive($vars['Itemid']);
 
			return $vars;
		}
 
 
		/*
		 * Parse the application route
		 */
 
		if(substr($route, 0, 9) == 'component')
		{
			$segments	= explode('/', $route);
			$route      = str_replace('component/'.$segments[1], '', $route);
 
			$vars['option'] = 'com_'.$segments[1];
			$vars['Itemid'] = null;
		}
		else
		{
			//Need to reverse the array (highest sublevels first)
			$items = array_reverse($menu->getMenu());
 
			foreach ($items as $item)
			{
				$lenght = strlen($item->route); //get the lenght of the route
 
				if($lenght > 0 && strpos($route.'/', $item->route.'/') === 0 && $item->type != 'menulink')
				{
					$route   = substr($route, $lenght);
 
					$vars['Itemid'] = $item->id;
					$vars['option'] = $item->component;
					break;
				}
			}
		}
 
		// Set the active menu item
		if ( isset($vars['Itemid']) ) {
			$menu->setActive(  $vars['Itemid'] );
		}
 
		//Set the variables
		$this->setVars($vars);
 
		/*
		 * Parse the component route
		 */
		if(!empty($route) && isset($this->_vars['option']) )
		{
			$segments = explode('/', $route);
			array_shift($segments);
 
			// Handle component	route
			$component = preg_replace('/[^A-Z0-9_\.-]/i', '', $this->_vars['option']);
 
			// Use the component routing handler if it exists
			$path = JPATH_SITE.DS.'components'.DS.$component.DS.'router.php';
 
			if (file_exists($path) && count($segments))
			{
				if ($component != "com_search") { // Cheep fix on searches
					//decode the route segments
					$segments = $this->_decodeSegments($segments);
				}
 
				require_once $path;
				$function =  substr($component, 4).'ParseRoute';
				$vars =  $function($segments);
 
				$this->setVars($vars);
			}
		}
		else
		{
			//Set active menu item
			if($item =& $menu->getActive()) {
				$vars = $item->query;
			}
		}
 
		return $vars;
	}
 
	function _buildRawRoute(&$uri)
	{
	}
 
	function _buildSefRoute(&$uri)
	{
		// Get the route
		$route = $uri->getPath();
 
		// Get the query data
		$query = $uri->getQuery(true);
 
		if(!isset($query['option'])) {
			return;
		}
 
		$menu =& JSite::getMenu();
 
		/*
		 * Build the component route
		 */
		$component	= preg_replace('/[^A-Z0-9_\.-]/i', '', $query['option']);
		$tmp 		= '';
 
		// Use the component routing handler if it exists
		$path = JPATH_SITE.DS.'components'.DS.$component.DS.'router.php';
 
		// Use the custom routing handler if it exists
		if (file_exists($path) && !empty($query))
		{
			require_once $path;
			$function	= substr($component, 4).'BuildRoute';
			$parts		= $function($query);
 
			// encode the route segments
			if ($component != "com_search") { // Cheep fix on searches
				$parts = $this->_encodeSegments($parts);
			}
			else { // fix up search for URL
				$total = count($parts);
				for($i=0; $i<$total; $i++) {
					// urlencode twice because it is decoded once after redirect
					$parts[$i] = urlencode(urlencode(stripcslashes($parts[$i])));
				}
			}
 
			$result = implode('/', $parts);
			$tmp	= ($result != "") ? '/'.$result : '';
		}
 
		/*
		 * Build the application route
		 */
		$built = false;
		if (isset($query['Itemid']) && !empty($query['Itemid']))
		{
			$item = $menu->getItem($query['Itemid']);
 
			if (is_object($item) && $query['option'] == $item->component) {
				$tmp = !empty($tmp) ? $item->route.'/'.$tmp : $item->route;
				$built = true;
			}
		}
 
		if(!$built) {
			$tmp = 'component/'.substr($query['option'], 4).'/'.$tmp;
		}
 
		$route .= '/'.$tmp;
 
		// Unset unneeded query information
		unset($query['Itemid']);
		unset($query['option']);
 
		//Set query again in the URI
		$uri->setQuery($query);
		$uri->setPath($route);
	}
 
	function _processParseRules(&$uri)
	{
		// Process the attached parse rules
		$vars = parent::_processParseRules($uri);
 
		// Process the pagination support
		if($this->_mode == JROUTER_MODE_SEF)
		{
			$app =& JFactory::getApplication();
 
			if($start = $uri->getVar('start'))
			{
				$uri->delVar('start');
				$vars['limitstart'] = $start;
			}
		}
 
		return $vars;
	}
 
	function _processBuildRules(&$uri)
	{
		// Make sure any menu vars are used if no others are specified
		if(($this->_mode != JROUTER_MODE_SEF) && $uri->getVar('Itemid') && count($uri->getQuery(true)) == 2)
		{
			$menu =& JSite::getMenu();
 
			// Get the active menu item
			$itemid = $uri->getVar('Itemid');
			$item   = $menu->getItem($itemid);
 
			$uri->setQuery($item->query);
			$uri->setVar('Itemid', $itemid);
		}
 
		// Process the attached build rules
		parent::_processBuildRules($uri);
 
		// Get the path data
		$route = $uri->getPath();
 
		if($this->_mode == JROUTER_MODE_SEF && $route)
		{
			$app =& JFactory::getApplication();
 
			if ($limitstart = $uri->getVar('limitstart'))
			{
				$uri->setVar('start', (int) $limitstart);
				$uri->delVar('limitstart');
			}
		}
 
		$uri->setPath($route);
	}
 
	function &_createURI($url)
	{
		//Create the URI
		$uri =& parent::_createURI($url);
 
		// Set URI defaults
		$menu =& JSite::getMenu();
 
		// Get the itemid form the URI
		$itemid = $uri->getVar('Itemid');
 
		if(is_null($itemid))
		{
			if($option = $uri->getVar('option'))
			{
				$item  = $menu->getItem($this->getVar('Itemid'));
				if(isset($item) && $item->component == $option) {
					$uri->setVar('Itemid', $item->id);
				}
			}
			else
			{
				if($option = $this->getVar('option')) {
					$uri->setVar('option', $option);
				}
 
				if($itemid = $this->getVar('Itemid')) {
					$uri->setVar('Itemid', $itemid);
				}
			}
		}
		else
		{
			if(!$uri->getVar('option'))
			{
				$item  = $menu->getItem($itemid);
				$uri->setVar('option', $item->component);
			}
		}
 
		return $uri;
	}
}

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