Can Japan be reindependent in this game?  Also, what about the idea of being able to split and become independent like Korea and Germany?

Japan starts as an independent country in the US sphere of influence and can choose to break free from the sphere over the course of the game.

But if the start was in 1949, wouldn't it be contradictory that Japan was independent at that point?  Japan became independent in 1952 based on a treaty signed in 1951.

Good point, I'm thinking Japan as a satellite of the US as the US never annexed Japan and the Japanese government remained mostly intact throughout the occupation.