You don't have the ballast resistor inline with the coil wires do you? You are using the orange and black wires for the coil and just have the ballast in line with the "switched on +24 V" wire to the MSD box telling it that power is on right, or where? I don't think you want to run the ballast resistor at all with a full MSD ignition unless you have it setup to convert back to factory quickly. The MSD sparks that coil a lot and I think it would be bad for a ballast resistor the amount of cycles being put through it by the MSD.