Regarding the usb panel connections, my thought was to just get some of these usb panel connectors that adafruit makes, seems like a good simple solution.
The patch bay is an interesting idea as well! Initially my thought was to just break the shield outputs into individual jacks and call it good, but a patchbay might allow for some more versatility.
Midi to cv output was another thing I considered, but hadn’t thought much about as I’ve got a Crow for that. Messing around with other power supplies (like eurorack or 500 series) inside the case might complicate things beyond what I could pull off, but it’s pretty cool. I really like how @klingklangmatze did this in his design, that’s a good place to draw from.