Try disconnecting the fuel line and run the engine off a gas can. You may have dirt in the tank (or a disintegrating fuel tank liner, if the tank was coated) that intermittently gets sucked up by the fuel pump.

BTW, I don't know how much the coil being upright has to do with anything. Chrysler mounted ignition coils upside down at the factory on the old flathead sixes and they worked fine.