I have a 1998 (new to me) 184,000 miles, 4.6l , runs rough , code is misfire on 3&4. Changed plugs, old ones looked good, changed wires, get great spark when I pull the wire off the coil pack on #3 but whether the spark jumps or whether I pull it away I get no change to indicate the cylinder is getting fuel. Injector clicks OK. Can a clogged Injector cause a misfire code?? Also got a low fuel pressure on rail two which I assume is unrelated.

 

Last time I had a misfire, I unplugged each injector wire one at a time to listen for a difference in engine tone, could easily tell if cylinder was good or not. What kind of plugs did you put in ? Everyone I know tells me to use Ford plugs in a Ford engine, plain & simple. You may have the R/H coil pack going on the bum, didn't mention if your misfire is always there or intermittent. Each time I get a miss, it's after I wash the engine......