Looking Good! Right on for using the original ports. It's the only way to fly.
I wish the Pi was around when I did my SNES, you have so much case room to work with and no concerns about overheating. Probably will boot faster, too!
Just out of curiosity, did you think of the microswitch for the reset switch off of my build, or did you come to the same solution as I did, independently?
Keep the hot glue going!