Also check your o2 sensors. I had a misfire in 2 and did the same kinda spot checks you did (swapped the plugs, plug wires, coils, so on). I got kind of a similar story about my fuel system but after swapping those out I got the same misfire code and the code stated I was also running lean. Turns out I had a bad o2 sensor on bank 2. I swapped it out and haven't had a code since. Turns out the bad o2 sensor was not only functioning improperly, but because of it only reading the small amounts it could, it was falsely claiming I was running lean. After talking with my local performance shop, I learned that for some reason the 5th/5.5 gens have really shitty luck with o2 sensors. I'm not saying this is your case but I would check to make sure of this also. A telltale sign is a rough idle on a cold-start.