As long as your meter is correct, I would have to think the PCM internal hardware is failed. The regulated 5 volt output should be 5 volts, give or take a couple of hundredths of a volt (4.98-5.02).
The 5 volt line has a 'protection' mode where it will shutdown the line if it detects over-current, like a short. Maybe it took a hit from the MAP?
Replace the shorted MAP and the damaged PCM.
A flash can't change the intended application or core identity of the PCM. A 1997 JA/JX 2.5L Federal 50 state emission PCM can't be flashed or made into a different year, engine or emissions market. The PCM will always be what has been burned into the chip.
A flash only updates the existing software to fix or enhance program strategies for known problems. Chrysler still has to certify that any authorized PCM changes meet all government requirements. The part number will update when read with a DRBIII. After flashing, an Authorized Software Update label has to be applied both under the hood and on the PCM housing.
I would use this PCM as a 'trade-in' core for another PCM.