Hi 'new_gti_owner', welcome to the forum.
Thanks for the vote of confidence there Mark, I'll do my best to help, although this sounds like an odd one :-/
I think the first thing I would be tempted to look for is a vacuum leak somewhere, possibly a bad one. Check the condition of all those vacuum hoses and pipes, if they're drawing in air they could be messing up the rest of the system which is in turn attempting to compensate.
Also, have a quick check and make sure all the injectors are seated correctly. I had an injector that, for some reason, had pulled out and the car behaved almost exactly the way you just described only it was very difficult to get it to idle at all!
I'll have a look in my books later and see if I can find anything else that might help.
As Mark says, those holes in the box are a common mod to improve airflow and shouldn't be causing the problem.
Good Luck, you don't need that thing revving up like that on a cold engine