Are you talking about the general jam over the Emaj7 progression, the solos, what?
I've just been taking on this tune in earnest in the past couple of months, and in general I find that the E major is it, but you have to stay off the tonic for the Emaj7 portions. Use the D# a hell of a lot and all will be clear, young jedi.
For the other parts - the Emaj7->B and the Emaj7->B->A jams - I follow the chords rather than the scale, introducing those notes not found in the Emaj scale incrementally where appropriate.
Sorry.. it's late and what I've given you is about as clear as mud.
- on edit -
Actually, I thought it though the beer haze and I stay with the Emaj scale, but use the B and the A as the "tonic" during that progression.
Still, instead of playing that decending bent F# into E as the intro lick (which a lot of people do based on what they *think* they hear on the studio cut), try going to the D# and play from there. My band bases all our transitions on the E D# C# waterfall.