That is really low miles. All the dealers and SA's are trying to rip everyone off. Tires should be replaced with tire shop, not at dealer IMO.
1. It is, but you did not have to agreed.
2. Depends on how you handle the issue, and what it said in your estimate of repaired. You came in for a specific problems, and ended up $3000 out of your package, not to mention problems still persist. I would first discuss with the service manager at this point to correctly fix the problems you first came in for. Ask them if the repaired were directly related to your problems, the answer will be either yes or no and go from there. You've got to be firm and reasonable with them, and not to take their next $3000 advice. If this does not solve the issue then talk to the GM. Find out where to file your next complaint if you have an unresolved questions regarding service.(Department of Consumer Protection in your area)
3. Focus to resolve on 2
4. Hard to say. I don't think BMW will considering a goodwill work on 2007.
Good luck. Come back with resolve.