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The diode idea didnt work I just tried it. And a solenoid wont either do to it needing a power loss to kick it off and nothing losses power with the alt powering it. I guess I will just run the alt wire and msd directly to the bat itself. I do like the idea of fuses on both sides of the alt line. And for what it's worth I tried the msd on the back of the alt and with the new box it didn't die either. Maybe because it's digital and not analog like the old box. I don't know why with the old box it would kill the car.

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Is your alt a single wire(hot only) or is it using
a external regulator.. if it has a external regulator
you have 2 field wires... one is a sense wire and
the other is keyed hot.. if you break the keyed hot
lead you then kill the alt... here is a simple wiring
diagram of how the system works