@cjohnson26 I have set up a working PS3 controller for RetroPie on my PI 3B+.
It is however an original PS3 controller from purchasing the console a few years back.
The instructions from the github page you reference are not as fulsome at step 3 as they could be.
I recommend the following additional thoughts in case you haven't applied them.
3a. Reset your controller, this is a little hole on the underside of the controller that you stick an uncurled paperclip or similar into. Do not touch a button until further notice.
3b. Once the PS3controller driver is installed, you must select it to configure options.
3c. Choose your particular (compatible) controller from the list, hopefully it is there.
3d. A screen will now appear asking you to plug in the controller. Plug it in for 10 seconds, do not touch a button!
I believe at this time certain configuration files are created, including for retroarch.
3e. Unplug the controller and now press the PS button. If working, the lights will 'sweep' back and forth, rumble and settle on the controller number.
You then start ES and configure the controller.
The default setup is pretty good for retroarch emulators, although you may prefer to switch X & O!