I'd take what TNVIPER had to say,
And you specified having replaced and cleaned fuel related parts, so it could be where this problem lies. I'd guess injector(s) failure or possibly bad plug, but you didn't mention any codes thrown. I'd back track to confirm they are all working. Did you feel a difference in performance prior to the change or after? Honestly, I felt a difference with 1 misfiring cylinder and my code appeared once. After I cleared it, it never came back but the problem was still there, and I was down on power. It was until I did my inspection that I found the problem. Now I feel all 10!
You have an 04' so unable to tell knock. Everyone who mentioned to buy a A/F gauge and fuel pressure gauge, they are right! Then you can narrow it down yourself if you are so inclined before doing a tune.