If it were stock, this symptom is caused by the bypass wire to the coil (used in the key's "start" position) working properly but the resistance wire to coil (used in the key's "run" position) not providing voltage to the coil. No telling how your wiring was modified to get both to the MSD ignition.
What happens when you put the fuses back where they came from?
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My Pontiac is a '57 GMC with its original 347" Pontiac V8 and dual-range Hydra-Matic.
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