1: The Overall Rating is decided on by use of the 4 percentages you setup on the AI tab in the setup page, otherwise with that not checked, it is based completely on the ratings on a player (though I do believe it is based on your scouted ratings, not "true" ratings, unless you have scouting turned off, or set to 100% Accurate)
2: I assume there will be more, however, this is one of those cases where I have a 2nd manager of no team, but is in Commish Mode, so I can go back and fix little ooopsies like that.
3: I haven't seen that happen to me yet (though, like you I've only done 1 season in the MLB quickstart so far, and in the first offseason, I had awards handed out.
Hope any of this helped a little.