Definitely go to Muir Woods on a weekday during the day (it can get pretty touristy during the weekends). Muir Woods is a grove of California Redwoods, which are spectacularly huge trees. You'll also get to go over the Golden Gate bridge and on your way back will have some great views of the city.
While you're in Marin County (north of San Francisco), you might as well check out a restaurant or two in Sausalito. Cute town, right on the bay, fun to just walk around in. If you are allergic to rich people I would recommend staying away though.
Honestly, just take a look at the Wikipedia article for SF and familiarize yourself with the city. There's so much to do and see here you're not going to be able to do it all in one trip. Heck, I live here and I'm still exploring.
Oh, and if you want good Mexican food, the Mission is the place to be. I recommend El Faroltio, which is right by the 24th and Mission BART stop. Some other places I like: The Blue Plate (dressed up American food, I like the meatloaf). Suriya (Thai, great curry). Wild Pepper has decent Americanized Chinese food. I would honestly recommend checking out
Yelp for places to eat. When you figure out what area of the city you're going to be in, just search on Yelp for restaurants near there and sort by highest rated.
Jam it back in, in the dark.
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