uXe I am down and would love to collaborate on this!
Believe it or not the project I am currently working on is something very similar but with regards to syncing the nesk-1 and cynthcart. I am working on updating the cynthcart code to send an 8 bit value out through the c64's user port. Then update the nesk-1 code to read that value through the nes controller.
I like the On/Off & Note # format you mentioned, and it would totally work for both projects.
Just brainstorming but would you be able to send a second value out? Then we could use controller 2 to change some settings via midi as well.