I have a 2004 fx4. I have recently replaces the timing chain guides,cam phasers, solenoid. It has recently started idling rough. Only after I have driven 5 to 10 miles. My bro, the ford mech. can't figure it out. His computer tells us that cylinders 5 and 7 are missing. The miss goes away when rpm's go above 1000. All new plugs and boots. We switched coil packs from cylinders that weren't missing and the miss still at 5 and 7 cylinders. Oh. We also checked the springs. They appeared fine. The engine knocks when this rough idle is happening but doesn't at warm up or while above 1000rpms.

 

did you figure out your issue yet? I have recently replaced the same parts you have and also have the rough idle. I have gotten a CEL for a #7 missfire but I cleared it and it never came back.

 

Actually going to work on it tomorrow. Going to replace the lifters for the #5 and #7 cylinders. Probably clean the throttle body too. It has actually gotten worse since I posted on here. It is starting to miss no matter what the rpms are. If that doesn't fix it I don't know what else to look at.