Again, you are not supposed to run a ballast resistor with the MSD. If you have been getting away with it, so be it, but I can tell you my car would barely run when I had the ballast resistor in the circuit with the 6AL2. First thing the MSD tech asked me was did I remove the resistor!

Sounds like you are not getting power on the small red wire during cranking. As I stated before, you need to temporarily jump that wire to the battery and see if that solves the problem.

I suspect that you have the small red wire connected to the ballast resistor wiring which (again) is not getting power while cranking due to a bad bulkhead. There is theoretically nothing wrong with doing it that way and long as you provide power during cranking and run.

The small red wire requires full battery power to run the box.