Throwing my hands up on this ignition!

People will hate me for this, but...
Ditch the MSD. Get a nice older chrome box, and new coil. And throw a spare ballast in your glove box.
My car wouldn't run right with with chrome box? Believe me I tried. It ran great with MSD that is when it ran. I should add this a built motor, 410 roller cam Eddy ported heads. The box I'm using isn't an actual MSD it's Summits version and I think it's working fine. I think it's something else that's the problem.