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Misfire 2006 Ford Escape

Yesterday had a check engine light on the vehicle. Hooked it up to obd reader and it showed three codes p0351, p0353, p0356 all of the codes were for the designated coils on the engine. I replaced all 6 of the spark plugs and all 6 of the coil packs with new. After the repair was completed I hooked the negative battery cable back up and the service engine light went out. I drove the car around and noticed a huge difference in the performance for the better. I shut the car off and started it again and the service engine light came back on. I hooked it up to the obd reader and this time it only gave me the p0353 coil code the other two were gone. I drove the car around and it still feels better performance wise except when I hold the throttle at a certain point to maintain the speed. RPM around 1500 that is when I feel a shutter going on in the vehicle, and if I increase the rpm by pressing accelerator more the shutter goes away and the car feels normal. I am racking my brain on this one any advise would help tremendously.