I feel your pain....experienced exact same issue on my 5.4L 3V. Literally spent thousands from the local mechanics parts cannon to no avail. I loved the truck and have it setup and accessorized just the way I wanted it. Being a stubborn old fart in my 70's, I wanted it to be my last truck. Boy, did I pay the price for that. I'm attaching a list from the parts cannon (please, no "what a ********" comments. I know, I know.
Resolution was reached by a young service writer at major Ford dealership during oil change discussion when he said..."Maybe you need a new set of eyes looking for the problem, we have couple of great techs and the equipment sophisticated enough to diagnose anything". I went home and thought about it. Came to the conclusion I had spent years and thousands to no avail. Made appointment with his Master Tech who was a couple of weeks out.
Received a call next day that he had it fixed but wanted permission to drive it home and back (about 150 miles) to be sure. Picked it up about 2 years and 45K ago and haven't seen the dreaded check engine light / misfire since. Had I taken it there in the first place, I wouldn't be writing this. But then I wouldn't have a truck where everything should be "good to go" for the next 230K. I attribute the cure to a very high dollar diagnostic machine and a great tech who was very conscientious and knew how to use it!
Here is the list of what was done BEFORE I brought it to the dealer. No one likes to spend $160 an hour labor, but it would have saved lots of money and heartache.
Hope this helps......
Maybe it's time for a new set of eyes on your vehicle.
Best of luck......
Planocat