Having owned 2003/4 LPs, and a pile of RX’s, and vintage guitars, just leave those pickups and enjoy. BBs from that era are great. Maybe, change out the pots. Caps you don’t need to, factory are fine.
Just play and enjoy it.
Thank you so much for following up on my request for an update! That is an impressive series of photos in the final products are fantastic. Well done. I’ve just finished a Les Paul junior build and followed many of the same steps you did. Melbourne….im just across the ditch here in NZ.
As has been said, in the middle position roll off a little neck pickup volume. In phase sounding. No need to flop a magnet.
with pristine PAFs unfortunately it’s best the leave them soldered factory fresh. I say unfortunately because they are tools but are now so valuable one should consider...