So i'm having some minor problems with the pickups on my JS1000... its like, the neck pickup (the PAF Pro) is too muddy, and the FRED is too sharp.. because of that, i cant' even touch the EQ on my amp coz if i raise the treble on the amp, the FRED becomes unusable, and the same for the PAF Pro if i put the bass up a bit.
what is this because of and how do i fix it? i want both pups to be similar in terms of their EQ, so i can use them effctively..
does this have something to do with the height of the pups??
please help me out.
thanks in advance
Ibanez JS1000BP
Fender American Stratocaster
Boss GT8 Processor
Korg AX1500G
Hmmm...hard to say without actually being able to check it out. Right offhand, I would say it might be bad wiring. Not to say that you, or somebody else, did a hack job but maybe the wires aren't routed exactly richt. With p'ups running four leads, and depending on how exactly your pots and switch are wired, sometimes it can get outright crazy trying to figure out which wire goes where.

So... I would suggest that you give DiMarzio a call tomorrow (check their website for the number) and ask to speak to Eric, or one of the other tech guys, and just explain to him what kind of setup (i.e. two humbuckers with standard 3-way switch with jumpers running to the switch, etc.). They'll be able to get you squared away if by chance your routing is off.

If the wiring is straight then I would definately take a look at the height you have them set at. Generally speaking the neck pickup should be somewhere around flush with the mounting ring, but not more than maybe 1/8." Where as the bridge p'up usually tends to be anywhere from 1/8" to 3/8" above the mounting ring. Now, keep in mind these general measurements are from guitars using Tune-o-Matic/Stapbar tailpieces.
BTW what amp are you using?
Ovation Celebrity
Ibanez Prestige S1220WNF
modded Ibanez GAX75
Fender tuner-DIGITECH EX-7-BOSS SD1-Ibanez CF7-Tech 21 TM 60
(LOOP)Boss DD20(Loop)
My soundclick page
i'm using a Boss GT8 for most of my sound, and just a practice amp for now which is permanently on clean...
Ibanez JS1000BP
Fender American Stratocaster
Boss GT8 Processor
Korg AX1500G