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I would try swapping coil #2 with on of the other ones and see if the misfire changes to the other cylinder. If it does you have a bad coil. If it stays on cyl.2 check the spark plug wire or fuel injector.
You have an interference motor. If you had to replace the heads due to the valves possibly touching the motor, you have to consider rechecking the compression after you replaced the heads. I had the same motor that had an intake leak. I found frozen rings on the number 1 piston as well as a bent pushrod. Ultimately, the camshaft had broken due to coolant getting to the bearings. If the spark is good, the fuel is good, then the only other problem you'd have would be compression.
What DTC code(s) are you getting?
You performed a compression test on cylinder #1; did you test cylinder #2?
Compare the readings, if there is a significant difference in compression readings between the two, you may have a bad head gasket, a bad valve, etc.
The bottom line, the problem is internal to the engine.
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.
replace the coil it is most likely bad. observe the engine at night or in a dark environment and proceed to use a spray bottle to lightly coat the coil pack for that cylinder number 3 and if you see an arc at the coil or any where else this will confirm a bad coil but even if you don't see any arcing it still may be a weak coil.
Has anyone found the problem? My 2003 has #3 cyclinder misfire and I have replaced the plugs and wires. It runs rough at idle but smooths out at highway speed. Anyone have any knowledge on this? This sounds like a common problem.
Could be a valve seat burnt, check compression, if lower than the rest, probably that or a head gasket leak next to #6. Borrow or buy a compression tester or get a garage to test for you. To fix you will have to determain wether the valve can be ground back in or a new seat is required, but either way, as it's a big job, get all the valves done as if one has gone, how long before more go?