Hey guys, i dont know if this could help you , but i had the same poblem on mine, did you ever cheked for the EGR valve ?

 

My check engine light began to come on as it ran rough, but would go off after the engine smoothed out.

It finally stayed on, ran a code and #1 was misfiring, replaced the coil and all good, no more studder and stumble.

 

I am having the same issue with Misfire on #1 replaced coil, plug and pack. Pulled the plug and found moisture in the cylinder. Ford told me might be blown head gasket. Put block seal in the engine and it cured the problem for a couple months. So I am having overheating issues. From time to time the water temp gauge will peg out on Hot.And so took it in to a firestone shop and had them replace radiator, thermostat and upper and lower connecting hoses. Came back with misfire on # 7 & 8 so had those plugs replaced with motorcraft plugs. Drove it for 5 min this morning and it pegged hot once again. So took it back to the shop and it came back with a code of 1299 engine temp over condition. When all plugs are pulled there is not water or coolant found in the chambers. Also had misfire on one. Had plugs in 1 & 2 replaced yesterday. Any ideas of where to start looking as to the cause to my problem and possible fix?