I would just skip bart altogether and just drive into the City. There is paid parking at pier 36. Driving time without traffic us just over an hour and 20 minutes. You will spend alot more time at the at Bart and Bus stations.
You can see just about everything from there. The bad side of being a tourist in this area is pick pockets. Keep your wallet where you can feel it. I tried to warn a friend of mine who went last year and his wallet was taken while on the cable car... He did not even feel it... Don't let it scare you off just be wary....
If you don't have one already get a cheap Garmin GPS from Costco $99. They are great for getting around in places you don't know... Easy to use and have a attraction feature for landmarks and things to see...