Basically your best options are a passive bass cut, a passive treble cut, a black ice boost, phase switching the middle position.
If you absolutely need to have mods, I would suggest replacing the tone controls with two push pulls, one puts a passive bass cut on the neck, the other gives the "Arlo cocked wah" mod on the bridge. You could try the Eldred mod for something simpler, but I prefer the Arlo, it essentially gives you a band pass filter on the bridge pickup that cuts treble and bass.