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Similar problem here, my 2000 F-150 HD edition, 5.4L has developed a sporatic miss. My check engine light came on at first, said misfire on 1 and 4 cylinder. I changed all the plugs and in doing so found that 3 of the 4 on the passenger side were wet and rusty. Ran good at first then started missing a little again. Cleaned the K&N filter, replaced the fuel filter, still does it. Checked the resistance in the COP's, read 7 OHMs consistently. CEL hasn't come on again. So hopefully someone has an idea out there. I'm stumped.
Mike what you may have to do is take the truck to your dealer and have them run a power balance test on it. This can be done on the road too with their WDS scan tool/scope. It usually shows which cylinder is missing quite easily.
How did the COP boots look? If there was water and junk in the plug holes I wonder if you have a COP with a corroded end. The boot comes off and then you can see the spring that fits onto the end of the spark plug. Sometimes these get corroded.
Had the balance test run and paged thru the history. I have been proven wrong in that a BAD COP does not always throw a code. Number 1 and number 3 were random mis-fire culprits. Changed them and all is well. RACERGUY was correct again about the power balance testing, seems to be the only way to go when a definite code is not being thrown up.