I am using USB midi so don't need it on the board and don't need I2C for the audio card as am using the onboard sound of the motherboard and also don't need pins for display as using hdmi.
So literally just the pins for the rotary controls for now.
If I can implement the serial connection with the board inside the C code (instead of wiringpi) then it may be the easiet option, however I would have to write from scratch as there are no C libraries available as of yet for that board.
The gpio board has an stm32f302 controller on board, so implementing an alternative via an arduino seems counter productive when the board is essentially doing the same thing already so the suggestion about usb <> serial integration in zyncoder from c0d3man seems to fit the bill as this is how the board already works.
I have the rtk.gpio python library downloaded so will have a look at the serial code in there to see how involved converting the protocol over to C would be (i can then retain all of the other zyncoder code mentioned above)
Ideally this would be an add on library to zyncoder (like a plugin)