What plugs did you use??

O e motor craft

Ok good. Did you check for any vacuum leaks around the intake once it starts missing? Is the engine light on and giving codes? What are all the codes?

Only code is cyl 3 misfire. Checked for air leaks with carb cleaner and used a smoke machine. No signs of air leak. Even replaced intake gaskets just to make sure. Cleaned mass air flow as well.

Just to be sure you replaced the coil, the plugs, and injector on that cylinder? Did you use anti seaze on the plugs? If so you may have used just a touch to much and that plug isn't grounding. Now depending on which 3.0 you have (ohv or dohc) depends on what you have for ignition so do you have a coil pack and plug wires or a coil on each cylinder? Either way what I would like you to do is if you have plug wires move # 3 with another wire to see if the miss moves with it if you have coils then move the coil. If that the miss don't move then move the plug. If that don't move the miss then I would like you to ohm the injector and give me the reading ok.