I have played around with the input and filtering caps and would now like to shift up the frequency of the clipping portion of the circuit when in high gain mode. Any suggestions for a starting point?
i'm not sure i totally understand what you're asking for. Do you want the pedal to sound brighter in high gain mode?
A lot of this can be controlled with C4 (the capacitor not the explosive). If you decrease or remove C4, you'll get a lot of brightness added. To make it switchable, decrease C4 to say, 100pf, then solder a 220pf cap between the legs 1 and 2 of the CRUNCH pot (not the hi-gain). This make it switchable, 320pf (approx. stock value) on crunch, 100pf on hi-gain.
these are just some values i made up, you can adjust to taste (in fact I recommend doing so).