Great h, glad everything is working now!
Below is my full xwhatsit firmware-related instructions which will be part of the upcoming Model F manual:
To install the firmware using Windows (I don't know about the other OS installation procedures), after assembly you would install atmel flip, plug in the USB on the controller and plug it into the computer, then go to device manager, right click the "Atmel" device, click have disk, go to the Atmel Flip installation folder, allow searching subfolders, and install the driver, then load atmel Flip 3.4.7, click the chip icon "select a target device" and pick atmega32U2, click OK, then click the USB icon, click USB, click Open, then click File, Load HEX file and select Joc's firmware hex file (alternative debounce threshold 6), then click run. After it says verified/pass then unplug the cable, wait 10 seconds, plug it back in, wait another 10 seconds, then open xwhatsit's newest version of the GUI (0.9.0?) and if it opens then you were successful!
If you have never installed atmel firmware before on your current computer installation, you need to open the xwhatsit software utility, click tools - enter GUI bootloader, click Yes, and then do the above Control Panel - Devices and Printers for the Unknown device.
unplug and plug in again if not detected first time after flashing
if can't install, can also try shorting PROG on the xwhatsit controller and keeping it shorted, then connecting it to USB, wait 1-2 seconds MAXIMUM, then release prog. will cause error device descriptor failed if you hold it too long