Regarding #2... the ump said that if you go back and watch the entire game and his signal calling, you will see that it is no different in that play than throughout the rest of the game. Mike Scioscia's complaint was that the hand signal made by the ump was akin to what everyone else uses to say that a batter is out, while the ump says that the signal was the same as how he called the rest of the game. I dunno.
But you can't do anything about it. This will just go down as one of those ubercontroversial plays. Why argue it? It's set in stone. Controversial plays have happened throughout professional sports. If Instant Replay doesn't exist for baseball, why worry? They can't recall it.