The Audi tranny will be turning the wrong way and you can't flip an Audi trans' R&P. Your looking at a lot of wasted time and money here, but as long as your having fun right?!
OOOOH, maybe you've decided to go mid-engine? Well if that's the case I'm all for the Audi tranny. 5000s seem to be a very strong and inexpensive option. Of course your still only rear wheel drive, but that's OK. How about attaching to Suby motor to your Audi trans? That would be a killer combo. I might try that one next. Sti and Audi seems to be a good fit huh? Of course there's the custom rear suspension to be designed and built, and you've still got to deal with the fact that the front end is a seriously oldschool design, but if your only going autocross you can bend the trailing arms to dial in some serious negative camber.
Jason