charging issues

The main things that cause a severe overvoltage/ overcharge such as this are:

Bad regulator

the voltage drop problems that I"ve mentioned in the harness and ground circuits

The "green" connected brush being grounded, IE the blue field wire, being switched ignition, then feeds "full field" to the alternator = full output all the time

Sometimes a bad battery

Your coil / and or ballast may or may not NOW be damaged, but given the symptoms, I'm sure that you have an overvoltage problem, causing the ignition to draw excessive current. You may be overthinking the ballast--they DO run hot, too hot to touch.