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Scott,
Check out page 36 of your MSD manual and it will show you how to install the diode that will prevent this run on. On Internal voltage regulated alternators it is different from external but the problem is still the same. You are keeping the MSD box energized by the tiny bit of the charing current that is bleeding back into the electrical system from your charging indicator light. That is why your symptoms seemed to go away after the reg. change but they will probably be back.
Use a (1A-100V) diode avail at radio shack and it should correct your problem. If you need a diagram or have lost your instructions check their web sight.
Good luck!
s
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