I didn't research 100% on this, but it looks like 1990 and 1989 YJs had the delco style alternator with the serpentine belt. The alternator body looks physically larger so you would need the mount also.
It looks like a bolt on retrofit. Very much like an HEI distributor. the wiring should be easy. I retrofitted an internally regulated Delco in place of an externally regulated motorcraft on my 74 CJ and it was easy. Its a popular swap and there are lots of write-ups with the wiring that it needs. I just followed those.
As for the PCM, all you should have to do is disconnect that wire energizes the field, I believe... I would compare and contrast the alternator wiring schematics for the two different years and try to copy the delco style.
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