Losing switched power and other #$%&^# electrical issues. HELP!

What are you using for an alternator/ regulator? If this is a GM "3 wire" you need a diode or lamp or resistor in series with the excitation wire from the "key"

With the problem "active" try pulling the small red loose from the MSD and if it kills the engine, AND THEN the "run" wire is cold after engine stops, then this has GOT to be some sort of backfeed issue.