Two-1/2 weeks? Heck, I could spend that amount of time just walking the streets of San Francisco and gawking at the architecture and the people and the views. Make sure you walk across the Golden Gate Bridge when you're there. There is no more marvelous thing to do in the entire state of California, maybe in the entire U.S. (well, the Brooklyn Bridge comes close).
I'd second Phil's recommendation of Amoeba Records on Telegraph Avenue in Berkeley. There's also a store on the far west end of the Haight-Ashbury district, but the Berkeley store is a bit better. While you're in Berkeley, take a Walking Tour of the architecture, especially the work of Julia Morgan that you'll see all over town and on the University of California campus.
Much of California is usually pretty dry in September, but there's still a lot of snow in the Sierra. It might be nice to drive across Donner Pass on Interstate 80 to Lake Tahoe, and down U.S. 395 to Mono Lake, and then across Tioga Pass (California Hwy 120) to Yosemite. The views of the Eastern Sierra from U.S. 395 are spectacular. I love Death Valley in the Spring, but I'd stay away in September.
A trip to Monterey and Santa Cruz would also be nice, and then drive back Calif Hwy 1 from Santa Cruz to San Francisco. The Skyline Drive is another beautiful route down the Peninsula from San Francisco to Santa Cruz. U.S. 101 north of San Francisco is also a beautiful drive. 101 south to San Luis Obispo and Avila Beach (my favorite beach) is another nice drive.
I still can't believe I got paid to drive up and down this state for 25 years. There's so much that's beautiful and interesting here.
Big Sur is indeed spectacular, but Highway 1 in Big Sur washed out last Spring, so I don't know how far you will be able to go in September. This page (click) will give you updated information. It's worth your time to drive as far as you can go, but you might be better just driving the 17-mile drive in Pebble Beach and visiting Point Lobos State Park just south of Carmel - those two places equal what you'll see at Big Sur.
I still can't believe I got paid to drive up and down this state for 25 years. There's so much that's beautiful and interesting here.
-Joe, in Applegate California-

P.S. I've moved this down to the non-music section because it seems to fit better there. Check the San Francisco Folk Music Club for music information - there's lots: http://sffmc.org/