I am a tech at a ford dealer . I have run across a few 5.4 's running rough. I have found the right side head cam timing was off by one tooth causing them to idle quite rough at idle with your foot on the brake. But they run fine off idle and have plenty of power. One tooth is just enough to affect the idle without hurting performance. These triton engines are very tricky to time the manuals say the timing mark on the right head should be @11:00 and the left should be @12:00 they state the marks should be approximately 11,12 . Well approximately some times ends up 1 tooth off. Best way to ck the timing is hook up SBDS run a relative compression test if all cylinders on one side are 4-5% low the timing is 1 tooth off. Hope this can help somehow. Good Luck