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I wrote a long response then lost it somehow. So brief version:
Avoid staying in Tenderloin where cheapest places are. Gritty, esp at night.
Go to Alcatraz, it's popular but very good. Book online before you go!
Hire a bike (at least one of the big tourist bike hire places that are all over the wharves can do a road bike) and go over Golden Gate Bridge v. early to avoid crowds. Then do at least hilly loop round headland, up Hawk Hill/Conzelman Road/Bunker Hill. Not far, very scenic, tourists can't hack it. Extend to Mount Tamalpais/Muir Beach if you have time.
Been quite a few times so let me know if any specific questions
chez_jay
Looking to go to San Francisco for a week in October. Where are the good places roughly) to look to stay and where should we avoid?