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I think there's feedback issues with disabling the alt outright. What you might have to do is set up a small cap bank (using the 300 farad caps maybe?) to take on the role of allowing current through so there's no feedback on the system.
It's my understanding that if you just straight disconnect the alt from the battery during operation it can seriously screw up the diodes/regulator, and that an alt that doesn't have a charging load doesn't take any power to run, so this might be the best way.
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