I have not done it myself, but I'm pretty sure that with that transmission you can swap the flanges from a 5-speed 986 transmission. The flanges on that Audi transmission are spaced wider and take larger bolts than the '97 axles.
Check this if you haven't already seen it:
http://986forum.com/forums/diy-project-guides/56663-audi-transmission-swap-diy-thread.html
It should bolt to the engine. Have you looked at shift linkage and mounts? I'm not sure about those. It might have the same attachment points.