if your car has 90mm flanges, and you want to keep the mk2 suspension, you either swap the 100mm cv onto your existing axles, or swap the flanges off the mk3 trans for the ones in your car now. unless your car is already 100mm cv equipped. then the axles hook up. but if you use the mk3 axles also, you also gotta use the control arms and some other suspension component up on top of the strut, otherwise you get some gnarly camber.
as for the VSS, take it out, throw it away or sell it, then install speedo cable.
you may have to do something about the reverse switch. early mk1's, late mk2's, and mk3's all had the same style reverse switch. small round switch with a 2 wire plug coming off it. so if you wanna put a MK3 trans in a late mk1 or an early mk2, you gotta do something about that switch. there is nowhere to mount the big 5 and 6 pin switches.
and as for used head gaskets, if i took the engine apart, the head gasket was fine, and i was putting it back in that same engine, why not? but i wouldnt take a used HG from one engine, and use it on another.