PCM Acting Up??? Advice

So I have a 96 XJ, we just put a 2000 motor in... Ran great for a while until I noticed no battery charge while running... My first thought is alternator, tested bad and we replaced it. New alternator, charged battery.... crank it, runs at 12.5volts still. Turn it off and try cranking it back up, it won't do anything... seemed like ignition switch then crapped out. We bypass switch and turn the starter over to verify starter solenoid, works fine... This has been on and off for a while... and only code I am getting is 12 55, saying battery has been disconnected. I can't figure this out and its getting frustrating. I have cleaned grounds and posts tightened all bolts... no difference. I will say we found a short in a wire that was grounding out/smoking, we fixed that before all this but there is no telling how long it was grounding out for... Would that have killed my PCM, voltage regulator is controlled in PCM correct?

That's a tough one BLK. I can understand your frustration. If you were to reference a wiring diagram, could you tell exactly what wire was shorted and repaired? Looks like that may be a clue to follow up on. I suppose you could pick up a salvage PCM and try it or maybe you have a buddy that has a spare?

Or maybe somebody has a technical definition of what the PCM looks for before it sets a code 12.

Good luck and let us know what you find out.....

Thx.... Anyone else? I really don't want to buy a new PCM w/o knowing if its bad or not, anyway you can test these things.... I hate electronics

What PCM are you using the, 1996 or the 2000?
I am trying to understand how you used a 2000 motor with distributorless ignition. Did you change all the engine wiring harness and PCM with the motor? Or did you somehow convert the 2000 motor back to a distributor driven motor.

A couple of questions:

When you turn the key on, will the radio and other accessories (like windshield wipers) work?

Will the headlights come on if you pull the switch?

I suspect this may be simpler than the PCM. The short may have fried a fusible link. Let us know the answers to the above.

It is a 96 XJ with stock pcm and harness. The motor is out of a 2000 XJ, it was converted back to distributor driven ignition. After cranking it today, it ran wonderful at first, but after about 5-10 minutes idle and voltage drop a little and lights kinda flicker. So I turn it off to see if it will crank back up, and sure enough it does nothing. Oh, and the accessories will work, lights... radio. Im using an Optima battery from my ZJ and it stills cranks the 5.2 right back up when I used 5 minutes later. Im going to keep looking for a wire that may be grounding out.

I'm not familiar with a 96, as I have a 90. I don't know how substantial the differences are, but on mine the positive battery clamp has two wires - the large cable to the starter, and an 8 gauge wire to something called the starter relay. This connects to a threaded post on the starter relay, and all the rest of the power for the jeep distributes from this post via 4 or 5 fusible links. You might suspect a faulty starter relay or one of these wires going intermittent. I doubt it is the PCM, as I don't believe it is in the circuit that sends current to the starter (as least on mine I don't think it is, I'd have to pull out the FSM and look). You should really sit down with the wiring diagrams and trace out the circuits that are going dead on you. Twenty minutes with the FSM will probably tell you where the fault has to be to get the symptoms you're having. Make sure ALL of your grounds are tight and clean too.