Oh Dammit. . .

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A rod bearing noise would be more obvious when the engine is hot. It would most likely be completely silent when you start the car, but once the oil is up to temp, at around 2000 rpm light load, it would be scary. Also, you wouldn't normally have a miss with a rod bearing.

Again, pull codes. The computer is telling you something, probably important, so listen to it. I wouldn't be surprised at all if it was something simple as a bad lifter.
 
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.
 
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.

I'm thinking it could be that cause I did have a lifter sticking before . I didn't get a chance to pull the codes yet so I'l try Saturday. I don't even have 5000 miles on this engine build either. It's still on the break in tune so everyting is completly fresh. I do thank all of you for the imput so much. I'm gonna check tomorrow to see if it blew a plug outta the head too. It sucks having to work and have no garage lol