about the Peter Green Mod? - I noticed & confirmed from photos that one of the pickups had the pole pieces in the wrong position ( i.e. turned through 180 degrees & put in upside down) - That in itself wouldn't make the guitar sound out of phase in the middle position, which is why I asked Guy if it had the modification.
It would certainly add to the "honk" in the tone on that song.
I also thought he used one of the MK models on Going Home but I can't be sure.
From my own photos, my opinion is that if he has a capo on a Les Paul it is most likely a reissue rather than the '58 or '59 but I can't be absolutely sure of that either.
In general, from reading posts on the Les Paul forum people are often asking questions about the originality of a guitar, and pickups do sometimes break & need replacing, or get damaged when someone decides to take the covers off - My Brother even had a modern '60's reissue in which one of the burstbuckers had a broken wire in a coil- so much for quality control.