Chris, there was a Heavyweight Title Fight on 12-2-1896 between Tom Sharkey and Bob Fitzsimmons. It was billed that way due to Fitz beating Maher in his previous fight. Wyatt Earp was the ref and there was some controversy in the fight.
Thats the only one that I have run across so far but I will keep an eye out.
Young Corbett II fought several title fights in San Francisco even when he wasn't recognised as the true Champion.
Terry McGovern fought a title fight against Herrera in which Herrera claimed he had been drugged.
There is also a book called "Boxing in San Francisco" that you might find something in. Here is a link.
Boxing in San Francisco - Google Book Search