1998 F-150 4x4 4.6L... Had code P0303 Cylinder 3 Missfire Detected. Installed new plugs and wires. Now have code P0303 and P0307 Cylinder 7 Missfire Detected. Was carefull not to mix wires. Engine runs rough when cold then smooths out when warm. Miss is not all the time.

 

I know this might sound crazy, but I think you have a EGR problem. Anytime #3 is involved, the EGR can be part of the problem. Sounds like the EGR might be sticking.

 

check the injectors too. misfire is also fuel related, not just spark.