Here I incorporated some learnings from the intervening years.  Upgrades from the first revision included:

• Schematic and PCB layout completely redone but using KiCad instead of Eagle.
• Microcontroller changed from an AT90usb162 AVR to an ATmega32U4.
• Remove the serial Tx/Rx connector.
• Remove the reset tact-switch.
• Use smd components instead of through-hole.
• Connect with a USB type C connector instead of a USB type B.
• Have the PCB fabricated (JLCPCB) instead of the home-made copper-etch method.
• A couple of LEDs on the bottom of the PCB purely to visualise the gray code (Rev 1 had LEDs but they only barely shone through etched sections of the PCB).
• Generally improved and cleaner code (still using the LUFA library).

In action.  The LEDs are a fun way of visualising the gray code.

Here it is next to another project (macr0).