MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Ah, I see. I once bought a bag full of those small 6x6 push buttons I'm using, so I must get rid of them. ;)
The case is always a shot in the dark somewhat. For standalone things like clocks I prefer using a Arduino Pro Mini + rtc (google for "ds3231 for pi", they are quite small. Especially if you desolder/cut off the pins). But some people just use a single esp8266 and sync time using ntp, others prefer using a more simple Arduino Nano (no ftdi adapter required) and a somewhat bigger ds3231 rtc (like the ones I'm using in the pictures of this thing).
Already thinking about a way to mount the buttons facing up. That way I could at least make the height somewhat adjustable by scaling the case along Z only. But the one thing I'd be more interested in is giving the software sketch a massive cleanup. :)