Does anyone know if there are any big differences with a 90 2.2 and a 97 2.2?

Yes - the later 2.2's have single exhaust port heads - not as desireable.

 

GD

Anything that would stop it from working in a 97 Legacy, like the wiring- harness.

90 is OBDI and 97 is OBDII so i think there would be significant compatability issues. but that's just a guess from what i've read on here. might want to look into swapping the long block ony and retaining the intake manifold on the 97 if that's possible. or swap the 97 wiring harness onto the 90 long block.

 

the 97 won't have EGR where the 90 will, so you'll have to deal with that as well. plug the hole and remove the EGR stuff and that should be taken care of easily. but again..i haven't done it.

The longblock swap should work. I have a 98 longblock in my 94, the only issue is that the single port Y-Pipe pushed the rest of my exhaust system back 2".