2008 F150 Limited- just replaced the 5.4L Vin 5 engine (186,000 miles) with a used 5.4L Vin 5 engine from a 2007 Expedition (108,000 miles). Truck and engine ran awesome for about 40-50 miles. Truck then went into fail safe mode. Threw codes p2110 and p2107. Towed truck to Ford dealer as i read here after a motor swap, the PCM needs to be reflashed. Dealer concluded that throttle body was fine. Also all wiring from TB assembly was fine. They also tried to reflash the PCM but could not get it to reflash. They did pin point checks and concluded the PCM was bad. I spoke to the shop foreman and he told me that he could not guarantee me that replacing the PCM would fix the problem, so I decided to bring it somewhere else for another look. Before i did, i disconnected the battery for about an hour and reconnected it. Truck started up and drove fine for about 15 minutes and then went back to fail safe mode. Can anyone shed some insight what this issue may be before i drop another 800-1000 on a new PCM that may or may not be the real problem please?

 

Those are forced throttle codes, I would generally expect a 'bad PCM' to throw some form of P060X codes as well. The fact that it starts after a batt reset says the PCM is not fried. If it seems to run OK while its running, I would not think its the PCM but tough to say for sure.

My first thought is a pinched/crimped wire somewhere that got hung up during the swap leading to a ground issue or something similar.