hello axe2- stew/mac just put up a new video with pick-up expert Lindy Fralin. He talked a little bit about how the wrong PICK-UP HEIGHT can make a pick-up sound bad. Something about frequencies/harmonics(?) I wish I could provide direct link but if you go to the stewart/macdonald site it should be easy to find.

I don't know if that's any part of your problem but it might be worth looking at? My son/law plays a USA PRS with stock pick-ups and the clarity/definition is very,very good. I have several SE's and I don't feel any need/urge to change the pick-ups... I like them a lot.

With the really good amp you're using that USA should be a monster. Sounds like u might just need a tweak somewhere.Good Luck