Yes, running with low fluid levels in an automatic(or engine) will cause higher heat levels and high heat kills automatics, just like it does engines, both need to run warm for best performance, but above the "normal" range is when metals expand too much and you get problems.
Who knows how long it ran with low fluid before you got the truck.
So trans rebuild was a good idea in any event.
Very confused with shops actions.
Faulty PCM is really a long shot, and 50% of diagnosed "bad" PCMs are a mistake, lol.
EEC-IV is the PCM used in your '94, and there is no question that they can fail, it is just an unlikely failure.
Simple first test is: does the CEL come on with the key and then go off after a few seconds?
That's the PCM start up self test coming out OK.
If CEL stays on then you read the codes, if codes are not readable then I would suspect PCM issue but still test the "test port" wiring.
Good read here on tests using the PCM: EEC-IV
PCMs failure to run tests would be a sign of internal or software issues, requiring its replacement.