Okay. So the buttons for the X and Y functions are not working out. I reordered some of the silicone button pads and am redoing how the buttons are held in place. The A and B buttons are great, this is basically going to make the X and Y identical functionally. This involves some fun dremel work to grind down the grey button bracket to just two small plastic arcs for each button. This will make them sit evenly with the AB buttons and allow the silicone button pad to be mounted behind them.
Also if you're starting this project, don't use solid copper cabling for the wires. Use braided copper for god sakes. The solid copper wires are just too damn stiff and keep breaking out of the solder mount holes on the pi and the controller board. Really aggravating.
The audio is having some issues getting sound out at all, all I can hear now is the induced processor noise. A Low Pass band filter is being made, the capacitors just came in yesterday. On a happy note today is the start of fall break so hopefully I can get some time in actually working on it.
Finally, I'm adding in a separate button to kill the pi before I kill power. I keep losing configurations etc due to the controller board not working correctly and having to shut it down by simply dropping power. This is really bad for the OS and also aggravating for troubleshooting.
Here's some pictures from before I took it all back apart to fix the issues outlined above. This was without screws, and the screen is upside down again because the config file dropped, and lost the line I added to flip the screen. The foam from earlier has been replaced with cardboard from an engineering pad for a more distributed insulator and base.