Similar issues on my previous F150 with a 5.4. I ended up getting an ODBII reader with the torque app. It shows real time data. Misfire rates for the ford engines have thresholds that may/may not throw a code. But the torque app allows you to see that actual misfire rates and pinpoint the exact cylinder. Usually it's a coil pack. I actually started carrying extra in the truck and could swap it out in 5 minutes. One trick I did that seemed to stop the problem was a liberal amount of dialectic grease on on it before installing. The plug wells are deep on those engines and hold moisture which I think contributes to the fouling. After I started to do that, I never had the issue again.