Mark you seem to know a bit about what is going on. I think you're holding back on us.
When something like this comes up on a forum people are simply going to believe what they want to believe and the whole discussion tends to degrade...
And mostly I'm kind of tired of the whole "5.4 vs. 6.2" debate myself... but that does not mean I'm not curious about the engine differences.
I can give you this update: The very next night a 5.4 Raptor (running E85) and a 6.2 Raptor (running regular grade gasoline) made a whole bunch of runs on a dry lake bed in 4WD.
Every run on the dry lake started at a low-ish speed and ended at or past the the point the speed limiter kicked in. (Curiously, the 5.4 had a tiny advantage on the top end during the longer runs as the 5.4 speed limiter seemed to be set one mph or so higher than the 6.2)
For all intents and purposes, the Raptors were equal. On a track, the difference would be more which driver got back on the gas first out of the corner. (Not so curiously, the slight advantage here went to the 6.2)
No conclusions can be drawn except that these two Raptors under the conditions (about 100 degrees outside for one) ran pretty damn equally under full throttle acceleration.
That said... a "drag race doesn't tell all".
I have a 5.4 and have had the honor of driving a 6.2 Raptor off road. As many have said, the seat of pants feel of power between the two engines is not what you'd expect (and even much less so if the 5.4 is running on E85).
The 5.4 has been around a LONG time so what I'm going to say next is almost as counter-intuitive as what I've already said... the 6.2 simply feels more "refined" than the 5.4. The 6.2 has far less of that "hey-I-think-someone-put-a-rubberband-in-the-throttle-linkage" lag and just feels better... like it's always right there when you want it. Again, not HUGE difference... but definitely a difference.
My opinion is that Ford did an excellent job on the tune for both engines. With what I know now? Weighing all the factors? If someone said "you can upgrade your 5.4 to a 6.2 for $3000"??? I'd be driving a 6.2 if I had the $3000.
But I don't regret buying the 5.4!!! (And I'd like to think this is exactly what Ford intended... )
YMMV
P.S. In response to one of the earlier posts, my 5.4 not only revs to the redline without manual shifting, but it occasionally hits the rev limiter in first gear! Neither Raptor was shifted manually.