how are you getting your sax mic into your pedals?
have you checked out the settings listed on the bottom of page 63 of the manual? https://s3.amazonaws.com/com.eventide.downloads/Product+Manuals/PitchFactorManual.pdf synlead might work better than guitar..
With the pedal, I just have one EQ after the pedal, To dip 120hz & 1200hz, and to cut above 7khz.
With the H9K I like to have EQs pre and post pitchfactor (set to killdry), with another EQ on a separate channel for my dry sound.