Gotta start by replacing that 40 pin connector both male and female sides. Check the boards for cold solder joints at all other header pins while they are out. If that doesn't fix most of your issues we can start to look deeper.

Even though there were not any cold solder joints, I would still install a new 40 pin connector on both sides. It might be gone for now, but it will return.

Sounds like you are on your way to a fully functional game. Have fun!