I'm pondering this same thing. Whitbread seems to think the wiring harness is not that difficult: (
http://www.4btswaps.com/forum/showthread.php?42666-VW-TDI-Swap-info-guide)
Here's my conundrum: I have a 2000 Jetta TDI ALH sedan with 5MT that I would like to swap into a wagon. I would just sell it and find a TDI wagon, but I've already done head studs, new head, timing belt, and a Stage 2 clutch, so I can't stand to part with the drivetrain. (I know...I'm a stubborn fool.)
I've done a lot of reading on here and the Vortex about this and come across a variety of answers about everything TDI-swap related. Hard to know who to trust.
My questions:
I assume it would be easiest to find an ALH wagon with a blown motor, as it wouldn't require a harness swap?
I've found an 04 TDI wagon (BEW) with a blown motor for a decent price (albeit far away). Is that a good candidate for a swap? (I like the improved options of the 03+ Mk4's)
Some say it's just as easy to swap the ALH into a gas wagon as it is a BEW wagon because of the wiring harness - true? (there are also fuel lines and tank to consider, obviously, but probably insignificant relative to the rest of the job)
I could ask a lot more, but I'll quit there. Any help is appreciated. Certainly there is someone around here that has done this before...