I'd say "nay" on this one. I had done an auto-to-manual swap on an old Accord wagon. It was extremely doable because of a couple things:
1) i had a whole donor car with me
2) it was OBD1
3) a lot of the drill points for manual transmission mounting were visible
4) minimal electronics modification
5) relative cheap ($600 for donor car, $200 for new axle, clutch line, fluids, relays)
6) there was a nice step-by-step write-up.
I had a 2005 Legacy GT wagon 5mt that I wanted to drop a 6MT from an STi into. The transmission itself would've been $4000; add axles, diff, LSD controller, it was going to be expensive. In end I made myself content with what i had.
I just saw, on Craigslist, a guy selling his E39 wagon that was converted to manual; he sure mentioned how pricey it was to do the conversion. I'd assume the same for the VW.
I guess I'm biased because this is my first European car, and I've got my guard up in terms of maintenance and upkeep costs.