Just a note: I'm talking about using the harmony on the Whammy, NOT pitch shift! I also don't think (and am somewhat sure) like E_O that this is NOT a pitch shift, because you can distinctly hear that it's as if he's playing two strings at different octaves --> harmony! The pitch shift would simply shift you up and down the octave without that effect.
Anyway, I tried the WH harmony (octave up) and got a satisfying result for that section which sounded very very good (tried it in pitch shift one octave up and it sounds dead wrong). Hooked up the EHX POG I and tried again and I have to say, I think he's using the POG I because although my settings aren't perfect, the sound is much more authentic.
Also, I wouldn't really understand why he'd have a POG and NOT use it for harmony (which is much more advanced than the simple WH-1 harmony settings), but rather use the harmony from the WH-1 when he's only using that for pitch shifting.
Anyone who has a POG I, the "Edge settings" are almost clearly visible from the Barca rehearsal pics. Once you get the settings you can tell he's using that for Breathe, Magnificent, NLOTH, Crazy Tonight and MOS!