Well, it's been a long time, but I finally got around to completing this project

I switched things up a bit with the release of the Rasberry Pi 3 B+ with build in WIFI.  Found a driver to use the GPIO and MCP23017 GPIO expanders as gamepads.

https://github.com/Rhys79/mk_arcade_joystick_rpi

Made the lower box as planned.  Wired everything up to a permanent prototype hat and an MCP23017 expander prototype board mounted to the hat.  Mounted the Pi internally to the bottom plate with standoffs.  Cut a 5x1.25" notch in the back lower center of the lower box and use a chisel to create a 1/4" slot for the plastic panel to slip into.  Mounted the panel mount extension cables to the plastic panel and assembled everything.

I'll add pictures later, forgot to take them while I was assembling it and don't feel like taking it back apart right now.