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:
Audi transmission Swap DIY Thread
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.