So, this is to save some time for people looking to bind keys and the usual settings..

There's a configuration .exe file in the /bin folder of the root game directory. It's titled MGS2SConfig. To edit Key Bindings, go to the tab at the top right corner titled "Key Config" and you could also change other settings within that program.

I changed the screen format to 720p because the default is square and to do that I went to the "Starting Setup" tab. I believe the rest of the graphic settings are in Effect.