Which pedals, cleats and shoes are you using?
Do you have any aftermarket in-soles either custom ones or drop in replacements, e.g., Conformable, Superfeet, etc. ?
Has your saddle height and set back been checked either against the "standard" formulas (one size fits none) or by a good LBS?
What is your average cadence when cycling, i.e., do you spin at >90rpm or grind at <80rpm ?
Are you riding a geared bike or a fixie? If it's a fixie, do you do a lot of pedal braking and skid stops?