Just went out and swapped PCMs, and confirmed that when I put the '94's PCM into the '95, I get zero connection errors. I didn't start the car since I didn't know what would happen putting an automatic PCM into a manual, but I don't need to start the car to get errors randomly on the '94, so no big. So there does appear to be a problem inherent to the chassis somewhere, not inherent to the PCM. Time to tear into the ALDL harness as well as inspect all the grounds, perhaps this weekend.

Also, steveo, how does the "Transmission Perf Button Pressed" indicator work in EEHack? It shows up as "ON" constantly on mine unless I ground pin 13 on the grey connector, at which point it reads "OFF" until the ground is disconnected. From what I've read this switch is just a momentary switch with a ground connection, so perhaps it should be the other way around? Maybe it's different on an F-Body?