All you have to do is take the small red wire for the MSD 6AL and cut it.
I would cut it near the MSD box so that nothing else will be effected.
Then run one end of the cut wire to one of the small posts on the battery switch. Then run the other cut end to the other small post. This will stop the engine from running when the switch is turned off. Of coarse you will have to wire the alternator so that it charges the battery.

Digger73 (Mike)