I have a 92 Dakota with the 3.9 V6 in it and recently just replaced the transmission but it sat for like 2 months while waiting on parts, and recently I've been trying to get my battery to charge while the truck is running but when I put a multimeter on the battery while it's running it doesn't charge it will drop voltage overtime and even when revving it a bit it doesn't charge. I have checked the alternator and it was fine, I replaced it and it still didn't charge, does anyone know what else could be causing it too not charge?
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Replaced what? It sounds like you replaced the alternator.
Batteries die. Once their useful life is over they won't hold a charge no matter how good the alternator is.
I am unsure of how to diagnose things... but if the battery is good (most parts or battery stores will test them for you) then there is a voltage regulator in the computer that does fail on these trucks. That can be solved by adding an external voltage regulator. Look up posts in the last year or so by member Bronze he had to do that on his.