Swapped in a spare PCM that I have and it's not dying anymore. Unfortunately, it's a truck PCM that doesn't run well with the Jeep injectors/vacuum referenced fuel pressure.
I am working on swapping a 5.9 into my '91 Dakota using '92 wiring harness and a '94 van 5.9 PCM.
None of the 5.9's in the OBD1 era run a return style fuel system, they all went to the returnless system with the FPR at the tank. But my '91 is setup with a return style system and doesn't have an FPR at the tank. This means there isn't a factory 5.9 PCM I can run that would just bolt in.
My plan has been to run the '92 fuel rail with the return line but remove the vacuum reference at the FPR on the fuel rail. Assuming the resulting constant fuel pressure provided by the '92 FPR without the vacuum reference is that same as what the '94 returnless system runs (pretty sure it is), the PCM will be none the wiser that it is running on a return style system. If necessary, I plan to adjust the fuel pressure using a screw through the vacuum nipple, but I don't think it will be necessary.
So, I would pull the vacuum reference off your FPR and plug is and see if it runs fine. I bet it will.