Wow, lots to take in there, and these kinds of problems can seem overwhelming but don't let it swamp ya.
I have a way of keeping it simple, and probably won't give you a ton of "do this and check that" items but more eliminate one or two things at a time.
Full charging issues usually come from a large draw somewhere, like a short or a battery that won't take the amps the alternator puts out.
Have you disconnected the bulkhead connector and inspected it for heated or melted contacts?
This is a prime source of multiple electrical issue's
You might also pull all the fuses and see if the problem persists.
This will disable pretty much all the accesories, but may give a clue where the problems are coming from.
If some problems stop with the fuses out, then putting them back one at a time a testing again could point out more specifically where the problem circuit is.
Let us know your results.
