This might sound stupid to some of you gearheads out there, but to me it seems like it could just be a hung valve. I've had that happen (not with the new Mustang) but with older cars when I went to move them from the garage out to the driveway and didn't give the oil enough of a chance to heat up. The next time I went to start it, a valve would hang, (sticky) and I'd have a miss and no compression in that cylinder. After it warmed up, the problem would go away. I've had that happen with a Chevy engine, a ford engine and a Toyota engine. Needless to say, I don't just move a car anymore without giving it 5 minutes of running time before shutting it off.