Thanks for the compliment!...sorry that you're losing low end

that saddens my heart.
Are you using a passive or active bass? that tends to affect the outcome as well...I've noticed that when i'm using an older bass it reacts differently then when im using a newer one...and it sounds different depending on the bass...for example, a pbass tends to make the pedal growl more in the low mids and lose some smooth lows as compared to say a Jazz bass or a Tbird where the sound is smoother and remains nice and wooley. Maybe try a few different basses?
Also, try having the pedal louder than your clean signal and that tends to trick the ears into thinking that its bigger than it really is...