High volts

Sounds like your VR and alternator is working perfectly. I measure 14.3 V at the cigarette lighter in most of my cars when the engine is running and 12.6 V with engine off. Yours is controlling 14.4 V (relative to its case?) for the voltage it senses. It does not know the voltage at the big stud on the alternator. It just makes it higher or lower (via the field) until it gets the 14.5 V it wants at its sense lead (a proportional feedback controller). I am talking about a factory Mopar regulator, either the older 1-field wire or later 2-field wire type.

Your problem is in the connectors and harness. This is a typical problem and you can find many posts. You shouldn't have any appreciable (>0.2 V ) drops in the path from the alternator output to all loads in the cabin (measure in fuse box). There is a ~0.75 V drop across the ammeter at full scale (~50 A) in the final run to the battery. The bulkhead connector, key switch, and "fused junction" in the dash harness are the typical culprits. The 40 ohm from VR case to BATT- sounds way too high. Sometimes that is a bad touching of the probes. Better to measure the voltage drop with engine running. Verify that BATT-, frame, and engine are all well connected.

Your batteries probably weren't ruined. Over-charging just electrolyses the water into H2 and O2, so you just need to add distilled water back. Maybe if it gets too low, you can "sulfate" the plates permanently. Sorry, not a battery expert.