[ImperialCrown]

Did this problem begin right after the PCM & alternator failure? Do you think that the current issue is related to this event?
In addition to battery, an alternator charge 'AC ripple' can wreak havoc with sensitive electronics.
Many auto parts stores can perform a comprehensive electrical system test out in the parking lot if the counter isn't too busy. Ripple can also be observed on a scope. You want a nice smooth DC charge. Sometimes you can hear ripple on the AM radio band, sometimes not.
Review what was done on the past repair for clean, tight connections and contacts.

The best way to form a diagnostic path to take is to read the 'Possible Causes' for all the fault codes and see if they share any potential common possibilities.
I see 5 volt high and 5 volt low faults together which may not make sense at first. Highs are usually from open circuits and lows are usually from shorts to ground.
The PCM protects the 5 volt outputs by turning them off if it senses something that could damage the PCM or the circuit.
I couldn't find a P2803. It might or might not be important. We can let this slide for now.
The 5 volt reference voltage 2 shows up twice. No codes for the 5 volt reference voltage 1. The problem looks to be on the #2 string. A Br/Yl wire out of PCM C1 is the #1; 5v string. A Br/Or out of PCM C2 is the #2; 5v string.
The P1628-#2 'erratic' 5 v fault suggests an intermittent, poor connection or wire rub-through problem.

Continued below:

 

[ImperialCrown]

I doubt that the Cam codes are mechanical, but I've included this:

 

[ImperialCrown]

I am leery of 'refurbished' PCMs. Sometimes you are trading old problems for new problems. They cannot bench test the PCM for every possible contingency. Sometimes it takes a couple of tries before getting a good one.
There really isn't any serviceable internal components outside of an authorized FCA electronic repair depot. The PCM schematics & many of the parts are proprietary.
This problem could still be in the PCM.
It is also important to use OEM sensors. You can introduce new problems or still have the same old problems with a new part.

Possibly drive with a data recorder to record what other things were doing when the #2; 5 volt line fails?
If the problem is not in the wiring or sensors, it has to be inside the PCM.