I recenytly purchased this pedal new (like last week) but tinkered with it all weekend. Firstly, I think your problems are fairly unique and you may want to return yours or test another one..no only did I not experience what you described, I actually found quite the opposite. I noticed a slight increase in volume (which didn't really bother me, b/c many phasers are far more quite..see Boss PH2 or 3), and I noticed on the lower setting, it boosted the bass or low frequencies a bit (again, not enough to piss me off). You should go back to the store and demo one with similar pickups or if possible with your exact rig.
As for mods, I only found one and it owuld not really help your issued.Sorry
Guitars: (just a few)
2000 Gibson LP Special-P90's; 1974 Ibanez LP; Fender(s) - Custom Shop Teles (4), Strats, Acoustics; etc.
In>TU2>EHX Small Stone>
Loop 1>Dunlop 535Q Crybaby Wah>Ernie Ball VP Jr.>
Loop 2>NS2>Send>BF2>CE5>Proco Rat Original LM308 Circuit>
Loop Master Out>BD2 Mod>Maxon OD>NS2 Return>Line 6 FM4>Carl Martin Red Repeat Delay>DD20
NYC Pedalboards: Big Shot
Power: Dunlop Power Brick
Off Board: Fender Blender, SD Tweak Fuzz, Exp.Pedal(s), Ibanez LF7, Rack):Korg DRV-1000, Furman PL8II, Shure ULXS (UHF Wireless),OC2, EBow, MXR 10-band EQ, Fulltone OCD, Boss RC20 XL, and many more!
Amps: Marshall TSL602, Fender Tweed Jr. NOS, Marshall JCM 800, B52 AT100Triple Retifier, Marshall JCM 800 Cab-Vintage 30's, VoxAC30CC2X,