Okay,
After cooling down a few days I got my head clear again and worked on it again tonight for acouple hours.
I compaired the harnesses readings on my red truck to the readings from my brown truck (the one thats a low milage original truck) and they all were coming out the same. So I hotwired the regulator and it was toast. So I pulled one from another truck and everything is running, I believe, as they should be. It runs a constant 13.98 Volts at idle and 14 open throttle.
But as before, it would always do this, run perfect with no signs of anything shorting or anything, then in a couple weeks it will stop charging completely, then overcharge the crap out of everything again.
BUT we'll see.