OBD I to OBD II Conversion Issues

If you did the manual fuel sync method it should be close enough to rough decent. I have had my truck way off after replacing the cam sensor pickup in the distributor and it still ran the same. The sync is mainly used so the PCM knows where number one cylinder is, since the crank sensor runs on a symmetrical flex plate with no "missing tooth" like other more modern systems. With this system, on both OBD1 and OBD2 PCMs, you can actually start and run the engine without a cam sensor plugged in by jumping the wires for a random sync signal, and it still runs good enough to drive it home.

For the fuel pressure comments, understand that the PCM fuel map is set up to spray a certain quantity of fuel in a given amount of time that the injector is on. So if you change only the injector flow rate (different injectors) you spray an unexpected amount of fuel and the PCM has a hard time adjusting to that. Same thing happens any time the PCM flow rate does not match the injector flow rate, but also happens if the PCM and the injectors match but the actual airflow through the engine changes, like using a different camshaft or even a set of headers in some cases. That is when a custom tune is needed.
Thanks for posting all of this. It's nice knowing that I can find detailed information about the MPFI system that Chrysler used on this forum.
I came to the conclusion about the injectors based on what you said about set flow rates, duty cycle, dead time, and fuel pressure determined by the original tune. If anything is outside of spec, it won't operate correctly. Adjusting the pressure got it back into the range it needed. I think the 18.2 lb/hr injectors are being ran at a higher duty cycle than intended because the PCM is tuned for a 23.4 lb/hr flow rate.
The reason I converted to OBD II is the fact it is tunable for things other than stock components. My engine has a mild Comp cam, Hughes plane, and headers and it feels like the factory tune on both systems wasn't able to take advantage of those performance upgrades.