You have gone through and checked all the fuses ??
Sounds to me that the first (start) coil of the COR is not pulling in for what ever reason.
once pulling the truck in gear enough air to allow the switch in the AFM to close pulling in the second coil in the COR.
Giving it fuel it starts and runs fine till shut off.
Did the starter being stuck cause the start coil in the COR to burn out ??
**** COR Circuit Opening Relay