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Replaced fuel filter already throws two codes cant remember off top of my head, need to change plugs haven't done that since I bought my truck last year
Yes, the rubber plug boot that is attached to the coil. Only mentioned them because I have read on iRV2.com Ford chassis forum that some owners have just replaced the rubber plug boot and it cured their misfire problem.
Could be a multitude of problems that will cause this. Fuel trims need to be read while running to help diagnose the issue. Intake manifold leak, low fuel pressure, etc. Don't rely on internet guesses + throwing parts at the problem.