The best donor car for you will be the VR6 MkIII Golf or Jetta. That car will have everything you'll need. The B3 Passats are more common, and you can pick them up cheap, but you'll need some cooling hoses and stuff that are specific to the MkIII.

You'll still need to change the engine harness and the ECU because you're going from 4 cyl to 6. Same with the cluster, your tach is set up for a 4cyl... you'll need a 6cyl tach or it won't work.

Heres a link to the MkIII forum on the VW Vortex. The answers to all your questions can be found there

http://forums.vwvortex.com/zerothread?id=3370991

But just something to think about... the MkIII came from the factory with a VR6. For all the time and work of swapping a VR6 into a 2.0 car, you would probably be better served by just trading up to a car that already has a VR6. The parts for the swap (motor, transmission, wiring/ecu, shifter, and hydro clutch) are a bargain at a grand. And if you have a shop install it you will probably total somewhere around $3-4k (just hope it doesn't burst into flames... Lee knows what I'm talkin bout ).