John,
The Air & Space Museum is right next door to the Auto Museum and it's a much better take. I would make sure you have time to visit it two. Also, Balboa Park is where the San Diego Zoo is which is another great take.
Chrsyler Performance West
http://www.cpwclub.com/ has a car show in the fall in Van Nays, if this is the same time as your trip it's well worth the 3.5hr drive from San Diego.