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I have swapped like 4 ECMs into my 96 and never ran a crank relearn. I think that is only required for like 98 and newer. You did open the ECM access and swap that little module from the bottom right?
that module is the knock sensor, it doesn't have anything to do with the crank position, I haven't had to do a CASE relearn on a 96 PCM either, but the code he's getting is definitely CASE related.