I've found the perfect style of MIDI USB footswitch for my project:

http://www.instructables.com/id/Teensy-MIDI-USB-foot-controller-for-controlling-Mo

One of these (albeit on a slightly smaller scale) will pass MIDI control signals to the Pi to control the switching on/off of pedals in the software.

I could also like to mod this design to incorporate two potentiometers for Expression pedal input.