Final update for those who need it. We wound up swapping my engine wiring harness out for a used one. They no longer make a harness for these year models, so a used OEM one is your best bet. I found one on
www.car-part.com for around $200.
Mechanic continued to believe the source of the issue was somewhere in the wiring. After swapping that in, he was still having a few minor issues. He wound up wiring in an older version of the ODPA as his diagnostic tool could get more information from that unit than the current one. Found and made a few wiring changes that seemed to fix the issues. Plugged back in the old unit as well as my old PCM, and swapped in a new CPS. Everything seems to be running fine now.
Have put over 1,000 miles on it with no issues. Nice to have the LJ back in fully functioning order again (knock on wood).
My mechanic did say this one really tested his mettle. He has been a Chrysler tech for over 25 years, and owned his own shop for quite a while now. He did say the new aftermarket sensor aren't what they used to be, but this was not really a sensor issue, but more related to wiring and communication.
Bottom-line, hopefully you can find a good mechanic willing to work on something like this. This seems to not be so much about swapping parts in to fix, but more of making sure everything is communicating correctly with the PCM. All the parts seem to be fine (crown ODPA, aftermarket sensors etc.), but they don't seem to communicate well with one another by just swapping them in and out.
Dman182 - if you have not done so, I would recommend finding a mechanic that has the DRB III Scanner Tool that can communicate with our PCMs. First I would try to clear all the codes and re-sync the CPS and the Crank Position Sensors. This seems to solve most issues with the aftermarket sensors. If that does not work, the second thing I would explore is the part of the wiring harness that goes to the CPS. It passes over the oil dipstick tube mounting bracket on the passenger side of the engine block. Over time, that bracket may rub a hole in that harness and create a short in the wires that take the signal from the CPS to the PCM. That seems to be the next source of interruption behind the two sensors not being in sync.
Apart from those two fixes, it's going to be a head scratcher and will take some trial and error on the part of a knowledgeable mechanic.
Hope this helps someone in the future. I was out of my Jeep for eight weeks while my mechanic sorted it out. This was not a job he could work on while the phones were ringing and people were in and out of the shop. He had to spend some time afterhours working on this one.