I know that the chasis harness can rub on the rear valve cover and damage wires, had to tie mine out off the way, also when you open the hood and their is weather out water will drain right on the connector if you have a voltage regulater causing corrosion. Check you pcm harness where it connects look for corrosion and female terminals that look open might not have a tight fit causing poor contact . I dont know the pin location but checking continuity from the wires that go from the pcm or voltage regulator to the alternator to make sure their is no damaged wireing is another check

 

Well, I got off work this AM and the Alt started charging as soon as I pulled out of the parking lot. CEL was still on. Got home and pulled the Alt off and opened it up. Looks like the brushes were all but toast. Surprisingly it appeared that it was the original one with just over 211,000 miles.

Fastforward to 9am and the parts store opens. Have said Alt tested and it tests good. 15.2v output good ripple no problems. I buy a reman one anyway and install it. No more problem. PCM still in control of itself and the Alt. I left the external regulator inplace and just unplugged it for future use. Just in case......