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

The only two terminals on the ign switch that will be hot "cranking" is the yellow start wire and the old brown ignition bypass, "IGN2"

Both accessory and ignition "run" go dead during cranking. This is why you hear all the talk about jumpering IGN1 and IGN2 (traditional blue and brown) together when eliminating the ballast.

Your small red on your MSD is a "trigger" wire sort of like a relay coil.
That is interesting. I'll check the yellow and brown wires. Everything in the car seems to go dead on cranking, but I will physically check those two. Without cranking power to the red MSD wire the box didn't see hall effect and won't fire the coil. One I run direct power to that red wire the car starts and I can see the light in the MSD box flashing with each hall effect trigger.