Nice project!

I just started something similar with a 3D printed case. I’ll actually be using one of those cheap usb snes controllers and soldering the leads directly to the pi rather than messing with the GPIO pins, maybe something like that would be an option for you.

Kind of like this (although I’ve found a way to keep the controller PCB in-tact with my build):
https://learn.adafruit.com/pigrrl-raspberry-pi-gameboy/buttons

https://learn.adafruit.com/pigrrl-raspberry-pi-gameboy/wiring-buttons