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