Hello:
One of the best resources out there is Kathy Beals' book. Kathy was a long time volunteer at the CGS library. She does not have roots in San Francisco, but had responded to the questions of many who do. Someone finally suggested she write a book and she did! There is a wealth of information and suggestions of alternate records contained in it. It makes research of our San Francisco Ancestors a bit less frustrating.
A USEFUL GUIDE TO RESEARCHING SAN FRANCISCO ANCESTRY
A knowledgeable San Francisco researcher provides practical ideas for dealing with San Francisco's well-known research difficulties, many stemming from the destruction of records at the time of the 1906 Great Earthquake and Fire.
Kathleen C. Beals. Pub. 1994 with 2001 Supplement, California Genealogical Society, Softbound, 8 1/2 x 11" format, 60 pp.
http://www.calgensoc.org