Cambria is also a great place to visit… one of the most relaxing/laid back coastal towns IMO. One or two nights there would be ideal. The hotels along moonstone drive are a bit pricey for what they are, but I think they are worth it. You could knock out nearby Hearst Castle too.
Cambria is far from San Francisco; with all the spectacular places closer to SF, it wouldn’t be my choice,
You probably already know this but the Time Out guides are a great source for information about things going on around town at any given time (e.g., performing arts events, festivals, exhibitions, etc.) Here’s the one for SF:
http://www.timeout.com/san-francisco
Oh, and on my mega-list up-thread I forgot to mention the Asian Art Museum which is in a spectacular building and has an absolutely amazing collection. It is a must-see if you have any interest in the broad and diverse spectrum of Asian Art.
(I also realized that my comment on the Cambria suggestion sounded a bit harsh. It is a wonderful place but quite far from the Bay Area, and there are so many places in the Bay Area to see!)
If you like browsing in bookstores, it’s worth a trip to City Lights Bookstore–a great independent bookstore founded by poet Lawrence Ferghetti (A Coney Island of the Mind). You can spend hours in there.
I’d second going to the Farmer’s Market at the Ferry Building–it’s open on Saturday. The array of produce is amazing and almost all of it is organically grown. It makes you realize how much of our food comes from California. If you go to the FM, have lunch at The Slanted Door (wonderful Vietnamese food). It’s in the Ferry Building.
The Castro Theater has sing-alongs to classic musicals and Disney movies. People dress up in costumes and they hand out goody bags with props. Good silly fun!
Correction to my post # 19 up-thread: The Lady with a Unicorn is by Raphael, not da Vinci. 
It will be on display at the Legion of Honor Museum from January through April. (Not sure when your trip is).
A few other things to consider for a first time in SF:
Rent bikes in Haight Ashbury and ride out to the beach through Golden Gate Park. My favorite stops include the arboretum, the Japanese Tea Garden (now costs money), the bison field, and the old Kezar Stadium, original home of the SF 49ers football team.
Go to Baker beach, west of where the GG bridge hits SF and close to Lands End. The roads and houses along the way are worth seeing and a part of the city most people miss.
If you have lived a bit of a sheltered life, see a live drag show. I don’t really know any of the places since Finnochio’s closed.
Go to the Cliff House and the Camera Obscura. Since you are a climber, there are some bouldering opportunities just below there, better at low tide (we also found some good bouldering on a Point Reyes walk).
Ride a cable car. You can’t go to SF for the first time and skip this.
Maybe I shouldn’t advertise this on a public forum, but you can go up to the top of the DeYoung Museum for the 360 degree view without actually paying to enter the museum - just walk past the ticket counters to the elevator. Another option is to go up to the top of Twin Peaks, an amazing perch right in the center of the city.
Rent bikes, ride over Golden Gate Bridge to Sausalito, eat at a restaurant with a view back to the city (I suggest Scomas, but it’s been several years), and take the ferry back to SF. I think The ferry will also take you to Sngel Island, which is a place I’d like to bike but haven’t.
Alcatraz for sure and drive up to Sea Ranch. We used to stay there with friends and the drive up is beautiful. Even if you don’t drink I still think Napa is worth seeing.
Unless you’re a real history buff, I think Fort Ross is a waste of time. Interesting, but not worth making it a destination. If you have a strong stomach, take a whale watching trip. Even better than watching from the Point Reyes lighthouse or other places, but those are not bad if you want to stay on land. 1214mom had good suggestions above. Sonoma has a wonderful town square & restaurants. Makes a nice day trip from SF in conjunction with nearby Jack London state park that was already mentioned.