it could be a throttle body problem. Clean it up, then clear your engine of any fault codes using vag com.
Are you sure that you blocked off the air intake? Because it would have to be one hell of an air leak to keep it running when you've got it blocked off.
I would have a look for any hoses that might have been knocked off during installation, but as I said, I would give the throttle body clean a go because it won't do it any harm for one, and that solved my rough idling and stalling in one hit.