From what I read on another site... VW's auto transmissions are a real bugger to get working right in a non VW car. Sounds like they have a system bus sort of like CAN Bus and it causes real issues with integration?
A love the thought of this project if you could source a TDI motor at reasonable price. If, however, you end up into this project 8-10k with motor, then simply not worth it. You simply do not have the payload capacity in a YJ to make it a great overlanding vehicle. Sure, great in tight places and for shorts trips, but it really starts to suffer in longer scenarios or those that involve more than two people.
That all being said, talk of mileage in the low 30s to low 40s gets me really excited!