I have a Early 90s Washburn. I installed new EMGS into it. It sounded great and then all of a sudden it has a crunchy clean tone. I changed the battery, plugged a cheap guitar into same cable and amp no problem there. I sent the pickups back to EMG and they reported no problems found. I put in proven passives pickups and they have the same problem.
New pickups won't necessarily make your guitar sound better or sound the way you want it to. I actually have made this same mistake in the past, I wanted my guitar to sound better and installed a Dimarzio X2N on the bridge position of my old Washburn WR120 and it's sound got worse (way too much gain and high frequencies). Years later I replaced all the wiring, installed new pots and replaced the bridge pickup with the original low gain pickup. It sounds much better now. I strongly advise you to take your guitar to a trustworthy luthier, state your problem and ask his suggestions on how to proceed to fix your guitar.