So the 2 things you need are this:
http://marcusjenkins.com/wp-content/uploads/2014/06/ARDUINO_V2.pngand
http://soulsbysynths.com/wp-content/uploads/2015/08/miniAtmegatron-PCB.pdfD0 and D1 are routed to the USB port on the Uno. This is then used to read/write MIDI data. To use these pins, you'll need to remove all the UART (serial) code in MinHardware.cpp
It may be better to sacrifice a different D pin. Poss the play button on SW1 (D2).
The way the code is structured is:
MinHardware.cpp - just deals with the interface, it has no knowledge of the audio engine
MinEngine.cpp - just deals with the audio engine, it has no knowledge of the interface
Min.cpp - stitches the engine and the interface together
I would edit Min.cpp:
goto Min::hardwareSwitchChanged(unsigned char switch_, unsigned char newValue)
then
if(switch_==MinHardware::SW_PLAY)
use this to determine the state of the multiplexer
and change this code to alter: engine_.getPatchPtr()->setFunctionValue(***whatever engine function you want to tweak here***);
hope this helps!
Paul