I disagree with the way you did the alternator kill switch. The way I did mine was not to disconnect the output of the alternator but to disconnect the field wires.
I think of an alternator as working this way:
When the voltage on the battey drops below some number (say 12.4 volts) the voltage regulator turns on the field wires and the alternator pulls power from the engine and makes current to put the battery back above 12.4 volts. When the battery gets back above 12.4 volts the field wires go back off and the alternator just spins freely not pulling the energy through the belt and making power.
In your system I think: You disconnect the output. The voltage drops in the battery. Your voltage regulator calls for the alternator to put out more power. It turns on the alternator by turning on the field wires. Your alternator pulls power from the engine and makes power but the power doesn't make it out. So I think your alternator is running full time.
Think about it this way. Disconnect the belt from the alternator. With the field wires off the alternator just spins with bearing friction. With the field wires on you are turning a magnent inside a coil which makes it harder to turn. It is just the reverse of a small fan. Stoping a fan with your hand with power off is easier then stopping a fan with the power on. In the first case you are just overcomming the bearing friction. In the second you are (with your hand) overcomming the power of the motor.
In my setup I turn off the field wires. This forces the alternator to just free wheel. Not pull any power from the engine and use it to make current. Even though the voltage regulator is turning on the field wires I have them turned off with a switch. Now when going down hill (not EOC) I turn on the field wires and now the alternator takes power from the engine and makes current and starts to recharge the battery.
Hopefully I've explained it --- This is the way I think most modern alternators work.
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