This is my first post, so bare with.
I just finished rebuilding my 5.4 4v engine, and thing was initially fine, but very quickly started missing under load, quite the bucking feeling. My scanner was showing bad contribution on 5&6( at idle), so I replaced the coils, but no real difference afterwards. It feels like the plugs are missing across the board. No codes yet, but I'm thinking the plug gaps are too high. I set them per the manual at around .054 I'm thinking that may have been for the 2v or triton? Any thoughts out there

 

Did you use Motorcraft plugs?

There's a label under the hood that gives the proper plug type and gap. Consult it for the correct gap.

 

As I suspected, the coils were bad for cylinder 5 &6. However, we replaced 3&7 instead of 5&6, because we had the cylinder numbering wrong. I suppose it helps if you double check some of your basic assumptions.