Alternator/Charge Issues

I know this and similar issues have been addressed in other posts. I’ve combed through many of those and am still confounded. And sorry for the long post, but it’s been a long a bumbuzzeling problem.

My son bought a 1994 Isuzu Rodeo (6 cyl, 2wd, 122k miles), he drove it for about 6 months with no issues. Then on November 25th he was out and the car started having what appeared to be transmission issues. He parked the car and called me to come look at it. When I got there the battery was dead so we jump started the car using my vehicle. When the car was running the panel warning lights (transmission, charge, all of them) were flashing on and off at random. I tried to put the car in drive and it shifted REALLY hard. Not wanting to drive it that way, we had the vehicle towed home.

At home, the battery was still dead so we jumped the car using one of those portable battery/jumper units. The car started but as soon as I disconnected the jumper unit the car died. “Huh” says I. Tried it again, same thing. We decided to swap in an extra (charged) battery to get the car going. Car starts, no warning lights flashing, shifted the car through the gears with no issues, took it for a test drive and the vehicle drove as smoothly as the day we bought it, no issues whatsoever.

We got the voltmeter and tested the charge at the battery with the car running, there were only 12.5 volts coming into the battery from the alternator (we should read 13-14 volts at the batter when the car is running). I figured it was the alternator and put in a brand new alternator. There was no change, same issue, 12.5 volts at the battery. We have chased this issue and can’t seem to figure out why we can’t get more than 12.5 volts at the battery.
To keep a long post shorter – here is what we have done (all with no results):

• New alternator; tested the old alternator and it was putting off 13-14 at the local Auto Zone. Also, with the alternator in the vehicle and vehicle running, if I test the voltage coming off the alternator at the charge bolt with a voltmeter it’s 14 volts (positive lead on charge bolt, common lead ground to frame).
• Swap out and test the battery.
• Replaced the charge relay.
• Checked all wires coming off the alternator for short/continuity issues.
• Checked between the alternator and fuse/relay box in engine bay.
• Checked between fuse/relay box and battery.
• Let the car sit un-driven for a week, the battery does not drain, which also doesn’t indicate a short
• Removed all the fuses that we possible could, one at a time, with the car running and testing voltage at each interval to try and see if there’s a short in one of the other circuits.
• Disconnected the wire harness at the transmission to see if there was a short or other issue at the TCM.

None of these steps have made any difference and we’re still only getting 12.5 volts at the battery (the dash voltmeter also only reads 12 volts). The charge light on the dash works as it should (comes on at start up then goes out) so that circuit is good and there are no other warning lights.

At this point were down to replacing the engine control module, but before we did that we wanted to post and see if anyone had any other ideas.

Thanks in advance!