.. more than one way to do this swap.
If you want to use a stock EEC, you need a similar EEC ( with or without EGR depends on your application ), I would stick with a 90 PCM. The 94/95 SC have the automatic trans function so you would need a 5 speed PCM, and then they are wired slightly different, they have a DIS module part of the PCM harness, and the 89-93 have the DIS mounted on the Engine harness. Plus you would need to use the 36# Injectors and the later model timing cover / harmonic balancer.
The 3.8 NA PCM will not run the engine correctly without a Tune. THe 89-93 and some 94/95 Federal emissions are made for a distributor whereas the SC uses a Distributorless Ignition system, the 94/95 are built to control the Electronic transmission and the 96/97 have OBD2 functionality so you would need to have it wired up for the OBD2 setup, and then re-flash the PCM to get the SC tune and transmission delete. You could use any PCM if you are going to re-flash it or get a chip, but without that you are limited to using the stock SC PCM.
I would stick with the early model harness and stock PCM, but you could definately make it work with a different harness and PCM if you have everything wired correctly and a tune.