A restaurant recommendation in SF is Scoma's just off the wharf. They have valet parking for next to nothing ($2 in 2007).
Staying in SF is very expensive and a crime risk; parking priced the same as NYC. If you try to park on the street, there is a high rate of car breakins. Find a place to stay outside of the city if you can. Public transportation into the city-BART, CalTrain, ferry, works.
A trip to Angel Island will take a huge portion of the day; Alcatraz a little less time.
Consider Sonoma wine country vs. Napa. Closer to the ocean. Korbel winery is gorgeous, along highway 12 between Santa Rosa and Occidental, in the redwoods. Occidental has some eateries and is a cute little town. Negri's and the Union Hotel competed for attention in the 70s, serving multi-course classic Italian meals. I remember the courses-Minestroni soup, ravioli, salad, entree and dessert. OMG, as a young teen with a ravenous appetite, it was a delight. Off of Fitzpatrick Lane, in the hills above Occidental, is a tiny collection of old growth redwoods, called the Grove of Old Trees. It is a level walk maintained by the local community, where no one walks. I discovered it by sheer accident when staying with family on Fitzpatrick Lane.
Grove of Old Trees
Part of it is wheelchair accessible. If you walk just up the road from that place, you will be looking at a vineyard, privately owned no tourists, and from the top of the hill, if there is no fog, you will see the Pacific Ocean. This will give you a view of coastal redwoods that you will not otherwise have, and for free!
Drive out to Bodega Bay, on the Bodega Highway, and you will pass St. Theresa's Church, which appeared in "The Birds". There are places along highway 1 in Sonoma County which sell oysters, and probably serve them as well.
I grew up and spent 40 years in the Bay Area. I visited the Sonoma area many many times, lived in the East Bay, the Peninsula, and the South Bay (Sunnyvale). There are many offbeat ways of seeing the redwoods, avoiding the tourists in Muir Woods, etc. I have family who have lived in these touristy areas, and we loved "playing tourist" but learned how to avoid the traps. DM grew up in The City and I walked around The City with friends as a teen. It is not very safe these days, and there is so much outside of SF that is amazing to see. I've hiked around Mt. Diablo and Mt. Tamalpias, Tilden Park, as well as just walking down my street to fire roads in the East Bay hills and spent the day hiking. In 1937 my mom attended the opening of the Golden Gate Bridge and the SF Bay Bridge; in 1986 I attended the 50th anniversary of the GG Bridge.
daylatedollarshort knows of what she speaks, so PM her, myself, and other Bay Area folks for suggestions, then take your pick.