A few things I would try before replacing or modding anything would be: first - lower the height of the pickup and make sure the treble end isn't too much closer to the strings than the bass end. Pickup height can really change the sound. Second - adjust the tone controls on the amph. Roll off the treble and bring in more mids. Third - change the gain structure of whatever preamp or distortion you are running.

In short there are quite a few things you can do to adjust for this, you just need to experiment. Remember that any pickup you put in there will sound brighter than it will in many other guitars due to the lack of the signal going through a tone circuit.