I have a 2002 Ford F-350 with a triton 5.4L. It has a misfire but only under load. It doesnt happen in neutral. All the plugs are newer and replaced the coils over cylinder 1 & 6 and still has the misfire. It is not constant misfire. While driving it with misfire then run fine then misfire and so on and so forth. Running out of ideas of what it could be.

 

Focus on the #1 cylinder to start with. Swap the spark plug with #2, the COP with #3. Drive the truck and re-scan. Now, did the misfire stay at #1 (the problem is something else), travel to #2 (bad spark plug) or migrate to #3 (bad COP)?

Repeat on #6 once #1 is solved.