Couple things come to mind. Some of the 24v folks might have a better starting spot.....
Replacement alternator could just be junk. Alot of the replacement are for these engines. Rebuilding what you had would have been the preferred option.
The new alternator could have some really bad AC noise worse then the last one.
There are known OEM harness issues with grounding which include the alternator circuits, sounds like you need to complete the wiring mods to repair your grounds. When you get it to it you will find it amazing they make it as far as they do.
As a coincidence the transmission relay could be bad you can swap that with the spare one. Dont think so, but never know it's an easy swap.
Do a as found AC voltage check with the current Alternator. See what you come up with.
A bunch of us split our time here at the TDR and on mopar1973man.com, over there it's a few bucks to sign up for a membership the 24v has a lot of wiring diagrams and articles on exactly what you need to do for the AC issue.
If you get it all the wiring sorted you might wind up ditching the external regulator that could just add issues to the trans issues your seeing.
If you happen to still have your original alternator save it and get it rebuilt you can do it or you can have a local.place do it. Rebuild items are cheap.