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I've got a 1999 F-150 with the 4.6. It idles as smooth as glass and accelerates smooth but when it hits high gear it developes a miss. It isn't constant but sometimes it jumps pretty badly.
I have:
Replaced the plugs (Bosch) and wires.
Removed and cleaned the throttle body and cleaned the intake.
Replaced the PCV valve.
Ran injector cleaner through it several times.
Replaced the air filter.
Any help in tracking this down would be greatly appreciated.