You got it!! Took me a while to trouble shot that one. I THINK they did it on purpose because the engine wouldn't shut off with it switched around the correct way. Nature of the external VR and ammeter wiring of an FJ40, I've been told. Needed a diode in white wire line to the alternator to stop the back flow of current. Whatever the reason, it should be good to go now! Diode in place, engine shuts off, factory VR on firewall bypassed, and charging at 14.5+ volts when running!
I learned that the hard way when I was in high school. I wired in an Alternator in my Baja bug and didn't feel I needed to add in the idiot light like the diagram showed. When the bug wouldn't shut off with the key It took me a bit to figure out the light was an important part of the system and did more than just show if its charging or not. A diode does the same job as a light, for that purpose.