I'm assuming this is a DIS(distibutorless ignition system).If it is,the most common cause is a defective coil pack.Each coil will fire a pair of cylinders together on 4 and 6 cylinder engines(one "waste" spark,one to ignite the mixture).Try swapping the wires at the coil pack to see if the misfire follows the coil tower,or the same cylinder misfires(keep in mind that a check engine light means you will have to clear the code to get the computer to feed that cylinder fuel before you start it up again).If the other cyl on the pack now misfires(i believe 1+5 are on the same pack on a Ford engine),then the coil is bad(spark is "leaking"to ground).If the same cyl still misfires,try swapping a wire+plug from another cylinder.
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