@mitu OK I figured it out. Fist i got into Stargate on RetroPie and re-assigned the game controls to different keys using Tab. "Input, this game". F is fire, T is thrust, H is hyperspace, 1 is player1 start, 2 is player2 start, S is smart bomb, I is inviso, R is reverse, arrow up is UP, arrow down is DOWN. This makes my head easier to remember. Then I went back into EmStation, disconnected the USB gamepad and reconfigured the keyboard as main controller. I set key 1 as Start and key 2 as Select. I also set key T as B and key F as A. Down at the bottom of the configure menu I left hotkey blank and when asked, I selected Yes. I also went into RetroArch/Settings/Input/Hotkey Binds and made sure Press Quit Twice is set to OFF. So to exit the game now I press 1 and 2 together and it brings me back to EmStation. And when the Pi is in the cabinet (hooked up to iPac2), I can work through the EmStation using the Stargate control buttons and never need a keyboard or gamepad again.

I just got this to work and it does help making GnG much more playable!

Use the Hotkey+X combo to open the green settings screen. Find 'Options'.

I had to flip both 4-way and also analog->digital to get it to play well. It's not perfect since only an actual correct joystick would do that. But it's now completely playable so can recommend for others that are having this problem.

It's basically just: plug it all in and then set up your controls in emulationstation. If you're nervous about it, there are lots of tutorials on Youtube to familiarize and educate yourself. Make sure your encoder comes with a Sanwa connection cable, then it shouldn't be too hard.

Ok so this is solved. The good news is at least as far as I can tell the Sanwas don’t go bad after only a year of use. This was a wiring issue with some of the connections I made between the five wire harness and the wires to the usb encoder coming loose, ironically and randomly several at a time. I don’t always supervise the kids’ use of the arcade so it is also possible this wasn’t REALLY random, maybe one of the kids was particularly rough or lifted up the control panel lid and pulled some of the wires. All fixed up now! Now I have a few extra Sanwas for spare parts though! (Only figured out it was a wiring issue once I installed the new joysticks and problem was still occurring...)

@ChristianG Great Question. The truth is there is no good way to ground this unit, and I am not sure I would try. It kind of blows my mind that you were even able to blow the unit via a static shock. I mean yes I know it is possible. All of my teachers 20+ years ago warned me about it. That being said I have been in the low voltage industry all my adult life, and I have never seen anyone in real live blow a unit via static. I did not design the joystick board and I would have to look at it's specs, cut sheets, and wiring diagram to show you how, but you should be able to by grounding the main negative at the board. But do this at your own risk....

@clyde my encoders buttons and joysticks arrived today but im atill waiting on the wood for the cabinet to be cut out and post to me but once i receive it and get it all set up i will post some pics

Great idea to use a wooden storage box!

@stevefo Please read the wiki/documentation pages before posting here! The "issue" you have is answered there,even with some step to step tutorials.

@battlecat The detail on the front and sides are cut vinyl, I just designed them on my computer and cut them on our vinyl cutter at work, it's usually used for signage so the small off-cuts left over are idea for this sort of thing.