Lets see. A have no real experience(yet), but close to a year of research as I am doing to same swap this summer.
All-trac trans is a AWD trans, it has a yoke for a drive shaft coming out of the back of it. I would avoid it.
As for axles, everybody says use 2 drivers side SC axles (hella expensive and hard to find). Some people mod their MK2T axles with different outer CVs. Personally I am swapping over turbo hubs and suspension front and back. So I will just use factory MK2T axles.
Lastly the MK1 motor mounts must be entirely removed to fit the 3s motor in there.
Looks through these for more info:
Kirk's swap
turbo
Speed - Source - Shifter Base Bushing Kit