To me, my Xbox compatible controller doesn't work in the WebGL version, so that it works a little for you is some kind of improvement (even if it works badly). Gamepad control works perfectly in the windows version. But I think it is something related to WebGL, and I cannot do anything about it, sorry :(
Regarding the missing files, they are in the repository. It is easy to check. I don't know what happened with them
I'm not sure why it has not imported to you correctly the JSON library, but I developed the code with 2020.3.1.f1 LTS. And using the official NewtonSoft JSON library it needs to be compiled with Net Framework 4.0... (Microsoft one is shit) so I imported the project as a new project(I updated Unity, just today), and yes, it shows me this error. I solved it by removing the JSON folder that created the library by itself. I will remove it from the git repository in some minutes.
Thx. You're the first that has checked the code (apart from my Unity teacher, whose I give it a task). Quite weird unexpected issues!!!