Major update!
Mausberry power switch wired up to the switches. The slider switch is the original switch. It mounts on a pair of studs and mates into the recess seen on the right (white square). The reset switch housing I ground down and hot glued in a microswitch. Slider is wired as power, reset is wired as reset. The white and blue wires plug into the Pi.
I decided I wanted things to be as simple as possible, so I am only breaking out power and hdmi. Can't really see the power port in the pic though, sorry. It's a standard two pin connector, round-round. The HDMI is not on the same plate due to mounting issues
Inside that power connector is screwed on to a punch out plate that I made from some scrap plastic which was then hot glued (god I love that stuff) into position. The cord was then routed around to a decased USB wall wart. I pulled it out of the casing to make mounting easier. When it is all assembled there is a small USB jumper that connects this board to the Mausberry power circuit.
The RetroPie image has a GPIO driver called GameCon already loaded. It uses a kernel level routine to read gamepad input, with far less lag than a user space driver. It has to be activated though, and it required my Pi to have completely updated firmware. Not a problem though, just another command line and some waiting. Right now the system is only wired for Player 1. Player 2 actually just splits most of those connections, there is only one wire for P2 that goes directly to the Pi, the data line. I just need to splice some jumpers between P1 and P2 for the clock, latch, power, and ground. Then some shrink tube and all is good.
Everything I've got here has been tested and works - took the half assemble beast to a gathering the other day and it was played for hours.