Make arrangements for Alcatraz well ahead of time, like now. I have lived in the SF Bay Area for over 40 years, all my life, and I have yet to get on the Alcatraz tour because it's always booked. If you do rent a car, I would, make sure to opt for the insurance! Some of my favorite spots are actually outside the city, then again I do not care for the city... sorry SF residents!
Some of the "Vista Points" are really neat. My wife and I really like Sausalito, the other side of the Golden Gate, very relaxing.
Other Neat things to do in the City not mentioned:
Cable Car, kinda cool to say you rode on one.
Lombard Street
Drive over the Golden Gate and Bay Bridge
China Town
As for places to stay, can't help there... we usually just do day trips or stay with my uncle.
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