I've mostly abandoned this project, but nevertheless I decided to include here some things that worked, some that didn't, and a link to a sort-of-working code.
First - The MIDI + LCD controller didn't work. I cannot recall the exact error, but the reason, if I recall correctly, was the difference between the USB bridge and MIDI UART's pull-up vs. pull-down. If there'll ever be another iteration, I suppose working with a uC that has native USB + a separate USART make that much much simpler.
Second - I updated the hardware repository, to include my best efforts to fix issues with the first iteration. I actually think the mux & 64 button DI shields work quite well. I tested them with code that's hosted at these gists (1, 2). The code is dirty and uncommented,
but hey - that's better than no code, right?
Here are some pictures of the the boards: