You might want to consider going to the Pantera-Electronics brain. It is designed for easy replacement of the MSD unit.
There is nothing wrong with the Motorcraft brain at all. In fact there is a lot right.
The P-E unit does offer features beyond the stock Ford unit though.
I also clipped a harness off of the Ford unit to splice in to the P-E so that the Motorsport distributor would plug into the harness as if it was the Ford unit to.
I suppose that means if the P-E unit craps out, all I need to do is plug a Motorcraft back in?
The P-E is a plug and play even with the MSD distributor. It certainly will like the e-coil. Doesn't really matter the brand. The hotter the spark it throws, the better.
You might be experiencing the RPM limiter chip in your 6a shorting out and cutting off the spark?
I went through that too. It would fire sporadically with the power timing light but wouldn't start the car.
In that condition, the unit test that MSD gives you did show that the unit was good. How can it be good if it doesn't start the car?
To me, this business of how to test, and it showing good, and the installation instructions of installing the tach adapter that are wrong and not working on the Pantera, just emphasizes to me, why exactly I want no part of that company AT ALL.
The Pantera is not a car that you ever want to have to worry about the ignition on. Should you need to pull the distributor, you have to take seemingly half the car apart.
Keep your fingers crossed you don't drop the oil pump drive shaft into the pan too. Otherwise you are going to have to pull the drive line out to get it.
Dependability is what you want on ignition. Not an ignition that at best is a 50/50 deal depending on what day and time it is.
Trash the MSD. Better yet, send it back to them. Attach a note saying "thanks a lot, here's another one".
I went with this distributor. Ford Motorsport A341, for racing with reinforced roll pins.