Do the readable files on the MGS game not describe the events that take place in the NES games? Is not the ninja in MGS not the friend who was left to die at the end of Metal Gear II: Snake's Revenge.
While I haven't played all the way through Snakes Revenge, I think I remember the game leading you to believe that's who the ninja is. It always seemed to me that those readable files were previous missions that Snake had gone on before the mission in MGS and those files describe the NES missions.
I'm not sure what MG (MSX) or MG2 mean if they don't stand for the NES games.