First of all, thank you so much for the guide. It's by far the most detailed one I've ever come across. I also love the fact that you used Teensy instead of GPIO. I know you said in your guide you would have preferred GPIO, but the setup you have now is fantastic for Lakka (as opposed to Retropie) -- Lakka is really meant to use USB input.
Quick question, I was interested in replacing your analog sticks with these: https://www.adafruit.com/product/512
I noticed that they're a little larger (1.5"x1.5") as opposed to (1.0"x1.0"). The wiring to the Teensy should be very similar. I took a look at your case, and I think (based on the position of the holes in the PCB for the larger breakout board) that it should just barely fit. I can drill holes in a different position on the case.
I wanted to get your take on this before I proceed.
Thanks again for the fantastic guide and design!