Mike, I'm surprised you haven't caught the full-on Subaru bug. You were one of the engine swap pioneers with that VR6 idea of yours. You could go Subaru engine connected to Subaru 5MT trans! A 2.5 maybe?
Anyway, the cheaper way for a trans only is probably Subaru as Rich said, but either isn't too bad for the 5 speed.
Needs:
FWD Subie trans - pre-1996 - OLD and cheap, hard to tell the condition due to age, but at junkyards they usually let you swap them out if they are bad
OR (more common)
AWD trans - You would have to buy the locking spool for the AWD one but could easily make the end plate and sell the center diff for $. At a junkyard you can get older ones for low $. Newer ones can be $$$. Make sure it's old enough that it has stub axles.
Plus:
- two "female" Subaru CV joints (used ones from NASIOC or Craigslist, I got mine for $50). Green in color usually.
- labor to re-spline a set of 914 axles re-splined on one end for the Subaru CV. This is as good or better than the $$$ sway-a-ways. The price has varied widely on this, from $50 to $130.
- $30ish MR2 shifter
- a cable shift setup. (you can do it yourself, all the way up to Ian's kit which is high $300's.
The Boxster trans is pretty much the same as a Passat trans, so you could go that way. Mike Bellis can tell you what you need there.
Only thing is...the adapter plate will cost you almost as much as a used Subaru or Audi engine...
EDIT: I rambled on so long Mike already chimed in
.