I had the same issue when I started playing outside of the shred-metal area here and there, the Jag-Stang itself is a rather bassy guitar (one reason I like them a lot actually), the only thing different with me is the EMGs push the output up enough to fry the voice coils of some amplifier speakers.
Anyway, not to have veered too far off subject, but what I did was added a 0.2-0.4ish capacitor to the input and output leads of the volume pot (treble bleed), when I back down, I can literally eek a more Jaguar-like tone out of the bridge pickup by turning the volume down.
I heard there was also a way to use capacitors and/or resistors in the signal path from the pickup to increase or decrease certain frequencies from the guitar's output. I've never done it myself, but my high school guitar teacher used to have quite a few resistors linked up to the pots of his home brewed guitars.