Using 100 amp mopar alternator to charge batteries out of a vehicle

You may want to upgrade to the newer electronic regulator and see if it changes. The older ones were adjustable inside and getting harder to find or try the solid state version of the old style regulator. What do you mean by an "unbalanced system"? The car systems would develop the same issues your having which was either the alternator or regulator. How old is your alternator? if you take it to a parts store most can test it for you.