One thing about San Francisco...its a bear to try and park a car ANYWHERE and the traffic can be terrible! Since you've never been to S.F. before...I'd strongly suggest you take some sort of tour either through the cruise line or even a private one. You will enjoy your trip a lot more without the hassle of trying to find on street parking, (which is nearly impossible) or looking for a cheap parking lot (doesn't exist). Without being familiar with the city, public transportation can also waste valuable time better spent seeing something unique to S.F.
Your problem is not having enough time to see what makes San Francisco the great city it is. (Great restaurants, fabulous shopping, unique coffee houses, exciting original theater productions, etc.)
Since your time is so very limited...a paid tour is most likely your best bet to efficiently use the time you do have.