Kris, have you tried a short straight edge across some of the frets in areas that you suspect. A high fret will rock back and forth and stand out like a sore thumb. Shoot even a plastic triangle might show up something. You don't have the pickups too high? They might be pulling the strings down some.
I can't see where a pickup change would effect the strings. Gotta get dat Ibanez back in the game.