My gas to TDI swap went very well. I had some wiring help from a forum member on vwvortex that was relatively simple and mostly only the two harnesses from the engine compartment need to be swapped. Add a small power panel for the 109 and GP relay power, TDI ECU, gauge cluster (need an immobilizer delete at the minimum), power steering pump to rack hose, AC compressor hose, left the gasser tank in (for now, at least-it works fine it you gut the filler neck), use the TDI fuel sender, abandon a couple of the gasser vapor return lines, etc
You are in a good situation to do the swap since you have the entire donor parts chassis. W/o the whole car to yank parts from it would be a lot more challenging. Also since your donor chassis and potential finish car are the same year the chance of ECU/immobilizer "issues" with other controllers in the chassis are minimal. Everything inside my finished car including the obdll port work without ant chassis side wiring hacks.
Should really take the thread over to the "conversions" section of the forum. It's been done a lot. It's probably not "worth it", but sometimes we do it anyways. I was in the same situation. My 2003 was rearended and I found a nice 2003 1.8T car with bad motor (broken TB) for $500.