Use everything from the '89, wire colors and even ECM location changed, the engine wiring is dead simple though, I used the stock '90 harness on the turbo engine in mine and just moved the wires in the ECM that needed it (turbo engine problems, you don't have to worry about that). That part should be plug and play, crank sensor should be same connector and so should everything else so just use the '89 harness on the newer engine... On the engine the only connections should be EGR position, throttle position, IAC, 4 injectors, two coil packs, crank sensor, coolant temp sensor in the middle of the intake manifold by the injectors then the oil pressure and coolant temp gauge senders by the oil filter... take pictures of random stuff like vacuum lines before you take it apart, might have to change some things like the throttle body or upper intake to get the vacuum ports right... You can use either accessory setup, both are the same belt spacing but the wiring for the alternator is set up for the drivers side so no use changing that...
You probably know, but might as well do a timing belt at that point, get one for a '94 as that's different too, round tooth instead of square (changed in '92), it's non interference but might as well...