Reason that I was asking is that on Fords the power for the coil comes from the starter solenoid at start and is a full 12 volts. Once the switch is in the run position the power comes through the resistive wire to the coil and is around 9 volts to prevent burning the points on older cars. A MSD tech would have to confirm this but I think that you need at least 10 volts for the switching power and you were right at the border line when the Atomic was not controlling timing when the ignition was in the run position. When you added timing control to the Atomics task you went under the minimum requirements of 10 volts and that was why the car stopped in the run position. I am thinking that you have an older Fairlane by your user name and pic so my theory could be completely wrong.

Also in some model years of Fords that resistive wire is in the steering column by the ignition switch so it depends on where you are tapping switched power from as to whether you are getting the full 12 volts. If you have a voltmeter check the voltage that you are getting when the ignition switch is in the start and run positions to the coil. On older Fords on the fuse box under the dash there is a threaded stud that provides 12 volts switched and that is where I connected power to my MSD ignition box and Atomic ECU.

This was the only thing that I could think of being your issue based on the symptoms you were describing. Good luck.