If SF is going to be at the end of your trip, you may want to relax a bit and head across the bay to Berkeley. There is great shopping (MAC, Bare Escentuals, Aveda, Restoration Hardware(!), etc., etc.) and really great little restaurants on Fourth Street (BART to Downtown Berkeley, AC Transit 51). Or if you're into the organic thing, you can go up Shattuck Avenue and eat at Ches Panisse (they have a cafe above which is less expensive and AMAZING) or get some fresh raw cheese at the Cheese Board. There's also organic pizza and nice shops up there
Very relaxed atmosphere (no tourists).
If you're going to the MAC Pro Store in SF, be sure to check out all the shops on Union Street. Union Sqare (nowhere near Union Street) is great for shopping if you don't mind crowds and TOURISTS GALORE (though there'll be many fewer in January/February). My favorite store in the area is the Container Store (around the corner from Old Navy) and favorite restaurant is Sushi something (I can't remember the name, but it's below some gallery on Geary, I think) which has THE BEST plum wine on Earth (but not necessarily the best sushi -- go to Kirala in Berkeley for that)
You can catch the cable car right there on Powell Street, too!
The Ferry Building market is a must see, especially if you're tuckered and just want to get some fresh goodies and relax in the park or your hotel room, hehe.
I lived in SF/Oakland/Berkeley for five years but never got to see Alcatraz, and I regret it
I'd definitely check it out if you get a day with good weather. I'd absolutely steer clear of Pier 39 -- It's a smelly tourist trap. Better to visit Ghiradelli Square which is not too far, also on the water (with a better view) and has some decent, if overpriced, restaurants (but again, with great views!).
If you're driving down the coast on Highway 1 (which I recommend because it is GORGEOUS, if sometimes treacherous) stop at Moss Beach Distillery. It's haunted and serves an awesome Sunday Brunch!!!! And good food the rest of the time as well (I recommend the Clam Chowder with mashed potatoes - it's the best and cheapest stuff on the menu). Just below the cliffs that the restaurant sits on is an awesome little beach with TIDE POOLS!!! It's my favorite place in the world
HTH! If you need any details regarding how to get some place in the bay area feel free to message me and I'll be happy to help
Have a great trip!!
Marianne