From what you say I get the impression you mean your D, A, E are higher than the others.
All you need for a fix is a lowering of the left ( as you look at it from behind ) side of the bridge.
Or a raising of the pickup.
As a rule on my JS1000 I fret the high E at the 22nd fret and adjust the bridge pickup until it is approx 2mm from the string and I also do this on the low E of the bridge and also the high E on the neck pickup.
Then I fret the low E at the 22nd and adjust the neck pickup so it is approx 5-6mm beneath it ( too close on the bass side and it tends to boom too much )
Obviously your neck pup will be at an angle, but that seems to give me the best clarity.
Also I have the left side of the bridge sitting slightly higher than the right, whether this makes a difference I don't know, but as regards to feel I prefer more distance between the string and fret on the lower strings.
P.S. When I say the pickup being 2mm from the string, I mean the pup's pole piece.