Hi Scott - Any pictures of the shut off you are using and mounting location?I've had a battery shut off on every GT I've owned. never had a dead battery and never had to charge it. the only thing is you do lose your radio stations when you shut the battery totally off. I don't care, that's not the music I want to hear anyways! the music of the supercharger is all I need!! lol
I've don't think I've ever had an issue with that. if I did, it never affected the run or performance of the engine even with a special tune. works as a good security feature.. you can just turn it off and pull out the red keyYou also lose all the emissions self-test status. Doesn't matter if you don't have OBDII emissions but if you do you'd have to run the entire drive cycle.
I had a switch on the Cobra too. Needed it because the Cobra is the easiest car on the planet to hot wire. But all the switch did was sit on the battery so someone with a 10mm wrench could take it out in a couple of minutes. But that's what all these things are about: slow them down so they move on.