I need engine advice. My gen 2 Coyote is running really rough after start. It has less than 50 miles on it.

The problem happened after the battery depleted to 5v. After getting a jump start, it ran smooth for 3-4 minutes. I walked inside while letting the alternator charge the battery. When I came back, the car was off. I tried to start and that's when the rough idle appeared. It stumbles at low rpms for 10-15 sec and then dies.

Should I fully disconnect the battery and try the idle relearn process?

94 Mustang body
Gen 2, 2015 Coyote
Ford racing harness and Gen2 computer
Battery shows 11.5v now

The car stalled at low parking lot speeds two other times, but never failed to fire right back up. This is the first rough idle I've experienced (lots of idle time in the shop, just never drove it before today).

Initial OBDII codes were all for the low voltage condition: ECU, trans low voltage. I cleared them out and it shows no codes now.

Bulldog

 

I checked the MAF and verified the sensor was connected. I rotated it a bit so the wires weren't touching the radiator. I let it sit for 10 minutes, then tried it again. The engine idled fine for 30 seconds, then went rough again.

 

Relearn throttle pedal?