I chased the miss down in my old V10 for a long time. I pulled the coils, gapped and replaced the plugs.. still had a miss. Moved the coils around trying to isolate the miss with no luck.
I read on the FTE forum that I could change the boots and springs on the coils and decided that I would. I ordered new boots and springs.... pulled all the coils off and while pulling the old boots and springs off I noticed this....

Upon further inspection 6 out of the 10 coils in my 99 had similar cracks in the body of the coil.
I ended up replacing all 10 coils.
Problem with the miss... solved...
I would suggest pulling the coils and inspecting them for similar cracks.
BTW.. I bought Uneek Supply coils x10 for around $100.00. They had good reviews and really stand behind their product. They worked perfectly and were still on the truck (without a miss) when I sold the truck.
Here is a pic of these aftermarket coils...

If you ever replace the coils, whether Motocraft or aftermarket make sure that the springs inside the coils are firmly seated in the coils before installing them.
Thanks!
Jeremiah