I used OpenSCAD to create a template for my holes. Once I was happy with the placement I exported from OpenSCAD to a DXF file that I opened in Inkscape and then printed.  I'm sure if I tried I could have done the layout many other ways but this worked well for me and I like starting in OpenSCAD.  I included both the scad file and a pdf from Inkscape in the github repo.

I used the template to mark the holes and then drilled them stepping up several times from a small bit to the bit to fit the buttons. I also used a drill bit to drill a hole for the USB cable in the base and then a snip to cut down to the hole so I can slip the cable in.

The buttons i picked only have a short terminal on the back so best choice was to solder wires to the switches.  I just used some stands from some cat 5 network wire I had laying around. I prepped all the buttons before installing them in the enclosure. 

To keep wiring simple so I wanted a screw terminal breakout board. I was unable to find a cheap screw terminal model strictly for the Arduino Micro so I ended up getting one for an Arduino Nano that is similar but doesn't have terminals for all the pins on the Micro.  For my use the nano breakout board had all the terminals I needed. By using the internal pull-up resistors in the Arduino I didn't need to add any to resistors to the wiring.  I connected to the 2-7 terminals to and split the ground wires between the two ground terminals on the Micro.

See the github page for the code that I'm using.