v6 box won't work you'll need a diesel quattro box, you could fit a tt / s3 one but gearing will be way out.
other than that you'll need drive shafts (front)
exhaust system
rear diff carrier
rear subframe and trailing arms
rear suspension
prop
rear shafts and hubs
centre mount for prop
diff / haldex
rear end wiring for abs / haldex
petrol tank
pretty much the complete rear underside of the 4mo including boot floor
as mentioned above waaay easier to drop it in a 4mo shell