I had the exact same issue you described, started after I upgraded to the 4+ tune from LMS... Called them and they said it could be "spark blowout" from the extra boost and improperly set spark plug gaps, others here said its probably a misfire from possible combo of things that I fixed all at once.
First thing, change the spark plugs and gap them properly, something ford seemingly never did. The gap should be .035..
Second, and the most probable cause of your problems, there is a wire that is unshielded that runs vertically up the front corner of the drivers side head. This wire is the knock sensor and has been known to chafe on the sharp edge of the head causing a short and consequently triggering the misfire your feeling while driving down the road. WRAP THAT WIRE!
I had these symptoms 3-5 times a week, haven't had them in the 2 months since I applied these fixes.