1st of all thank you everyone for trying to help.... I hope I don't sound rude below..... lol
I had this exact same setup engine included in the 77 RT, with zero issues, I do have the coil wire insulated with aluminum foil with a heater hose wrapped around that..
If you saw the video below, if it shows, move the regulator to the fender and straight wired it bypassing entire voltage regulator wiring harness...
It has to be a ground issue somehow between the alternator and the engine (head)......
On paper you have done all of the right things. I applaud your work to insure excellent grounds. That is so often overlooked, even by the best mechanics.
My biggest caution is still that MSD system, and coil. I am sure you have had wonderful success on other builds with the same setup; heaven knows they sell enough of those units to somebody. I just know from a lot of years of automotive electrical experience that I have seen the same setup do some pretty unfortunate electrical things to perfectly good cars. The problems were finally sorted when one of two things happened, the MSD equipment was removed, or identical replacement MSD new equipment was installed, and the previous units were returned to MSD under warranty, and found to be defective.
In my world, Chrysler engineers did a darn good job wiring up these cars to be very reliable. It is my understanding you have pretty much rewired the entire Underwood area. Your skills, and methods are sound, but it will be hard for us to offer much more than the speculation that we have put forth since none of us truly know how far off spec your car is electrically at this point.
I actually saw a car one time that had welding wire from the battery to the grounds, and the alternator. In theory it should have been great, but actually had terrible charging fluctuations. We pulled the fat cables off as an experiment, and replaced them with the standard factory cables, and the car ran, and charged perfect. Don't under estimate Mother MOPAR.
Best of luck in sorting this through.