dunno how to rewire your pickups but would recommend you get some hot SCs from Tims range here.
Re the neck relief, a change from 9-42 to 10-46 will require a slight adjustment clockwise (more tension to the truss rod to compensate the higher tension from the thicker strings). Maybe 1/4 or 1/2 turn could already be enough. Go easy on the trussrod, don't force anything. Give the neck an hour time and retune again, as the wood needs some time to adjust.