As far as an auto trans to mate to a VW diesel;
I'll second earlier comments that trying to run a B5 chassis Paasat or Audi 4Motion / Quatro trans is NOT the way to go, too many differentials. Also saw one out of the car and cut away at the Detroit Auto Show a couple of years ago, and that transaxle is HUGE, and my guess very heavy.
Second problem mating a diesel and an auto trans is that nearly all of classic (1960s and 1970s style) Detroit auto trans used intake vacuum to adjust the shift points and pressures in the trans. Oops, a diesel does not have intake manifold vacuum, so one more work around to figure out.
If you want a classic all hydraulic 3 speed auto trans, I'd suggest the Chysler 904 TorqueFlite. Neither the small 904 nor the larger 727 TorqueFlite used manifold vacuum, you would just need to adapt the linkage that sensed throttle position.
If you want a modern 4 speed OD auto, I suggest the GM 4L60-E. In particular, I'd go with the one from a Chevy S-10 with the 2.2L engine. Bell housing is short enough to give room for an adapter plate, and small enough to clear the water outlet on the flywheel end of the VW cylinder head. No vacuum needed for the 4L60-E either, all electronic control, and aftermarket stand alone controllers for the GM trannies seem to be commonly available.
That is all I think I know.
Piper106