My 2006 EJ bridge pickup just seems to be a bit strident, with some sort of overtone thing going or a hot-output thing. The sound is not totally clean; it may be due to the string/bridge characteristics or ?? Backing off the volume or tone controls helps a bit, but that kills the sparkle and punch. Adjusting pickup height does not help. The other pups sound fine to my ears.

Your guitar need a profesionnal tune up . Did you check intonation first ?