Look out for mk2vr6.com. It's offline at the mo due to the guy who runs it is away travelling the world, but it is the font of all knowledge on the vr conversion.
You are better going for a 90 spec Mk2, preferably a 16v as the fuel pump can be utilised on the conversion.
If you can find a complete car for the conversion great, if you can't just go down the Corrado/Golf route, as the Passat is pretty rare in the scrappies/classifieds.
Parts you will need:
Engine
Gearbox
Pedal box - if you require to go down the hyd route, although you can use a Seat clutch mech.
Wiring loom
Subframe - Mk3 can be used only requires a cut down engine mount, but Corrado is a straght swap. Wishbones can be utilised for a wide track front end, but std Mk2 items are fine.
Brakes - you can utilise the Mk3/Corrado brakes too if you want to use the 5 stud hubs, but if you want to retain the 4 stud just use the Mk2 driveshafts and wishbones.
Gear selector mech
Radiator - Mk3 can be used, but the Corrado rad and fan set-up is a straght swap
You can use the Mk2 front cross-member but you need a Mk2 VR6 front solid engine mount. Otherwise go for the Corrado set-up, as agian it's a straight swap.
Don't worry about the rear axle, as they are the same. The Mk3 has thicker rear hubs giving it the wide track.
Can't think of much else at the mo, but any more q's drop me a pm and I'll see what I can do.
Lewy