It does sound like the chip or even something in the PCM itself. Do you have a complete spare computer you could swap in? I did not have any experience with the OBD 1 reprogrammable chips chips, any reprogramming I do is on the GM OBD 2 stuff.

To test the alternator, put your voltmeter on AC, one lead on the negative post of the battery not the clamp but directly on the post, and the other lead on the output of the alternator. Anything over 0.2 V is too much. You can see it more clearly with a lab scope but a voltmeter works fine. I haven't seen temperature affect it very much but you can check it hot and cold. You might also check the actual output, should not be over 14.6 V. And is always triple check your grounds.

I never had a PCM intermittently lose its memory, but have had several go "stupid" and require a key off and then restart sequence. Internal computer, stray EMF from computer and sensor wires being too close to faulty spark plug wires, and AC ripple voltage from alternators.