Hi Wasabi,
there is an solution without the core hack.
At first point on JFactory::getApplication(); it loads the default
Joomla admin site and installation scope.
register your custom application with
$obj = new stdClass;
// Custom Client
$obj->id = 3;
$obj->name = 'myApp';
$obj->path = JPATH_SITE.'/myAppRootFolder';
//expand it here if needet
//register an the new Application Scope Object
JApplicationHelper::addClientInfo($obj );
//getting the myApp
$myApp= JFactory::getApplication(3);
Does it helps you?