If you re set on Amtrak and that schedule you re out of luck. Amtrak doesn t have a train to suit your needs. If you can manage leaving early and coming home early the quickest/easiest route is to take Amtrak to Richmond and then BART into San Francisco.The most convenient way to get here is going to be by car. It s not much to rent one for the day.
Take Amtrak, get off at Richmond, from Richmond take the BART and get off at Montgomery Street. Then you can take Muni Bus 3.