Also, would it have been the SKIM not being programmed that caused the PCM to ground the fuel pump and EVAP purge solenoid circuits?
No, I don't think so. It may be a PCM fault aside of any SKIS issue. Generally, if there is a SKIS issue the PCM will disable the engine, not keep the fuel pump running.
Or what else could have made the problem with the PCM? I want to verify the problem with the PCM so that the new PCM doesn't have the same problem.
Before getting into SKIS at this time you can do a check of the ground signal from the PCM to the fuel pump relay socket in the PDC.
Remove the fuel pump relay from the PDC.
Plug PCM C3 back in.
Refer to the fuel pump circuit diagram above and the PDC layout above.
You'll be using a digital voltmeter for this check. First starting with it set at 20 VDC, then if neccessary, set to 2 VDC.
Look at the FP diagram. See the relay pin connector at the relay "C3". This is the ground control from the PCM.
Now look at the PDC layout. See the fuel pump relay socket pin "3". This is the same as "C3" on the diagram.
With the FP relay removed, key to OFF/LOCK, voltmeter set to 20 VDC.
Measure the voltage at the FP relay pin cavity 3 in the PDC, using the battery negative post as the ground for the voltmeter.
Normally you would see between .01 and .150 volts. If you see battery voltage (12 volts), there's a problem with the PCM FP relay control coil ground driver.
If you see a very low, or no, voltage, switch the meter to 2 VDC and see what voltage you get.
If you get no voltage at all at pin cavity 3 in the PDC, try at pin cavity 5. Some of the Chrysler diagrams have changed pin cavities from what would normally be the ground control pin cavity to how they wired the PDC.
If you do see the low voltage (.01 to .150), turn the key to RUN and read the voltage again. There should be very little change in the voltage reading from key OFF to key RUN (in a normal situation).
As far as the EVAP Solenoid cycling constantly, it should only cycle after the PCM enters closed loop (or thereabouts). The Solenoid gets a constant 12 volts (White wire) when the key is to RUN, and the PCM provides a pulsated ground to the Solenoid (Pink/Black tracer wire) to cycle (Duty Cycle) the purge valve. There's no way the Solenoid should cycle with the key to off. Even if the Solenoid ground control wire was shorted to ground it wouldn't pulse/cycle the Solenoid. PCM fault if it constantly cycles the Solenoid when the key is OFF.
Read the attached pages extracted from the 2000 XJ FSM about the SKIS. I've added a red bar in the margin of the text that you should read.
If you have any questions about the PCM you should contact the place you bought the PCM from and ask them about prepping the PCM for SKIS, and/or contact a Jeep service center and ask them about it, and what you should do concerning getting your Jeep to the dealer for complete SKIS programming.