Have you tried adding a line to the autoloader setup file ? I mean, something like this:
array(
'Zend\Loader\StandardAutoloader' => array(
'namespaces' => array(
'Zend' => $filedir . '/Application/Vendor/Zend/',
'MyCustomModule' => $filedir .'/Module/MyCustomModule/',
),
'fallback_autoloader' => $fallback,
),
);