Let me guess, you have between 75000 and 90000 miles on it (or possibly more if you have been lucky). You get a belt type squeal that goes away when the engine bay warms but will tend to show up when you come to a stop after driving on the highway in cooler weather. No engine codes will be found. If you have not already noticed it the "hick ups" will start to begin lower in the RPM range as the engine warms. IF I am even close, your syncronizer is on the way out.
I had a similar experience, did a full out tune-up, wires plugs, filters (all), buttoned it back up, and almost the next day on my way home from work I felt a tiny hick-up, so I pushed on it and the hick-ups got worse. I checked with everyone to figure it out as there where no codes. A friend hooked up the snap-on analyser and ran every perimeter possible and nothing. Put his had on the Cam position sensor that sets on the syncronizer and could feel it not running smooth. I took it to Ford (already had the appointment, could not get part in time to replace myself before appointment), Ford had TSB for this time of issue, basicly they monitor the EGR signal if it cycles over 150 or so to the max of 1053, it is a bad syncro shaft. The problem lies in the fact that the syncro is not monitored for fault codes over 2500 RPM.....IE Not CHECK ENGINE LIGHT or code to read................ :-( PS when the shaft fails completely the sensor strikes the housing stopping the shaft, shearing the shaft gear at the cam, and best of all stopping the oil pump.........wala new engine required.