I was able to figure this out and wanted to leave this for anyone else that might have this issue. Ended up looking through the source code and noticed an If statement that was not getting fired.
Change
$createdFile = $service->files->insert($file, array(
'data' => $data,
'mimeType' => $mimeType,
));
To
$createdFile = $service->files->insert($file, array(
'data' => $data,
'mimeType' => $mimeType,
'uploadType' => 'media' //add this for pdfs to work
));
It's just that easy! Hate it when it's that easy..