What woods are your Charvel made from?
I have a Charvel 475 (HSS) made from Basswood with Rosewood Neck fitted with a Nailbomb and two Irish Tours. This is how mine is set up.
First, set all three pickups to initial heights.
A) Humbucker: Fret bass E at last fret. Adjust so that the distance from the top of the screw polepiece to the underside of the string is 3/32". Do the same on the top E string.
B)Single Coils: Fret bass E at last fret. Adjust so that the distance from the top of the polepiece to the underside of the string is 4/32". Do the same on the top E string.
C) Adjust Bridge pickup first. I have found the trick here, is to only lower one of the screws to balance pickup. Don't go trying to tweak both screws at the same time. I.e If it sounds too bassy drop the Bass side slightly, or vice versa. Also, its small tweaks on the screw of about an 1/8 of a turn, if that.
D) Fine tune Middle.
E) Fine tune Neck.
F) Check that output of all three pickups are balanced.
The above worked for the aforementioned guitar but I suspect there maybe other twists on the theme for other makes of guitar.