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Answer 1: he supplies his own software to read the GPIO inputs from the joysticks/buttons. You can try and incorporate his software into your project (I think he provides it for free), write your own, or find another software option. Personally, I got the ControlBlock add-on board from PetRockBlock and intend to use that for my arcade joysticks/buttons.
Answer 2: lots of different options here. I believe MAME uses 6 buttons, two rows of three, plus a coin button and a start button. NeoGeo used one row of 4 buttons. Console emulators use from 2 up to 8 buttons depending on the system emulated, plus a select and start button. I’m still trying to figure out my exact layout. I think I’m going to go with two rows of 4 buttons (allowing up to 8 buttons for PSX), plus a start and select button, and possibly a few more, not entirely sure.
Answer 3/4: I used this article to learn about the options for sale: