> Does the engine mate with the Vanagon trans without adapter?

No.

> Can you use auto as well as manual trans?

Yes, but that would be two totally different adapters (as far as the
flywheel/clutch adapter is concerned). The adapter for "engine->gearbox"
could stay the same, I guess.

> Are you strengthening the gearbox?

I am driving the Audi V6 (not the VR6) for 4 years now. The gearbox is at
its end now, humming, scratching etc... (total of 230000kilometers, about
40000 with the Audi). Strengthening the stock tranny is no real solution in
my opinion.
I would take a Porsche or Audi gearbox (the turning direction can be swapped
on tiptronics)

Raimund