WOW...she definitely has boundary issues. I go through similar things with my ex's wife, and my son is now 13 and HATES her. She has serious control issues and tries to manipulate everyone in the house and now my son is starting to see it. I have tried to discourage him from thinking this way, because she is is step mother and isn't going anywhere any time soon, but he has figured it out on his own. It's so bad, sometimes my son refuses to go on his weekends there.
I think Hamster is right, if they are not married and you have custody you should be able to stop all the stuff that is school related. If she is driving past your house and causing problem at his baseball games, I would document that stuff. You actually might be able to file harassment charges against her, shich definitely isn't going to be in their favor when you go to court. Also, I'm not sure about the area you live, but I know here in Ohio it is considered a "mother's rights" state...which means the ONLY way a father can get full custody is if they prove the mother unfit. Have you tried discussing this with your ex husband at all?