[burnin oil]

I would unhook the alt and see if everything behaves. The internal alt has the wiring plug on the side instead of the back of the alternator. The plug should be a rectangle instead of the rear mounted square. The wiring plug is what controls the alt turning on and the output with the large wire on the rear controlling nothing. It is just the output lead that goes to the battery. If everything works normally with the plug off then you know it is the charging circuit. If the problem persists it is an issue with the new wiring. It could be a faulty ignition switch keeping power going to the ignition or a crossed wire somewhere or the ignition is picking up power from an always hot circuit. With new wiring you have to double check everything.

The ballast resistor is not needed as said before due to a resistance wire in the harness, atleasst the stock harness. Either way the ballast resistor is not needed. Its purpose is to lower voltage to the points during normal operation to increase their service life. During start up they get the full 12v from the wire going to the starter solenoid and around 9v during normal run.