I have a 98 f-150 4.6L w-Motor I was getting a code for cylinder 3 continuous misfire so I replaces the coil pack, wires, and plugs. It went away immediately, later tonight I went out to the store and it started what seemed to be a misfire again so I hooked my scanner up to it but it didn't pull codes. But... It only does it every so often and will then smooth back out so I tried some heet thinking it could be water in the tank , did nothing , what do you think the problem could be ?! Could it be clogged injectors, or low fuel rail pressure ?

 

Check the fuel pressure. If it is still missing on cyl 3 you could swap injectors around to see if the miss moves.

 

Take a close look at the injector connectors.