I had tried all 3 methods on my pi 3. I used the manual cmake steps, I had tried the wget install.sh method, and I had also tried the GUI option in the retroarch "optional package" menu. I ran into no errors during any method, but nothing worked. Nothing was responsive in jstest. When performing the GUI option pi 2.5, it worked. (I didn't try other 2 methods on the pi 2.5 as my first attempt worked).
I think its my pi. I bought it a few years ago and this was my first time trying to use the GPIO headers. I downloaded a pigpiod GPIO test script and it identified some of my pins as bad. I think I'll grab a pi 4.0 in the near future.
I made a video going over my gamepad design if anyone is curious.