Just a quick update:
Still working out one or two audio issues with the Zoom interface; everything works, but there's a crackly digital sound over the mic sometimes. I have a feeling it may need the JACK settings fiddling with and dropping from 96k, or having the buffer increased.
That aside, the concept is working brilliantly; inputs can be routed via JACK into the effects software then into Reaper, as well as directly to Reaper. This allows me to record clean and effects simultaneously.
The Arduino Due has had a basic sketch put on it to send CC messages from the buttons on an LCD shield. It works, and has been tested with triggering Reaper transport controls.
This is coming along nicely.