So I have built a Superheated SHO, and moved the Hot/Superheated switch to a footswitch instead of a toggle. Since it's on a footswitch I'd like it to switch without a pop of course. Would a 100uf cap going from 9 volts to the center pin of the switch, keep voltage on the circuit as it switches and eliminate the pop?
It won't help. Might hurt.
This pops because the voltage on the drain of the lower FET changes when you change from a resistor load to a Mu-stage load. If this were all carefully balanced, with the cap on the mu-stage load pre-charged, and the mu-stage JFET selected to make it all work out... maybe.
In practice, it's far simpler to make two of these, one with the mu-stage load and one with the resistor load and make the footswitch switch between them. Duplicating the lower MOSFET is easier than what you'll need to do to make the single one pop free.