:hi:
I am a 5th generation Californian and I've researched the areas you mention extensively.
The town of "Sisson" is the town of what is today called "Mt. Shasta" in Siskiyou County, California. It was known as "Strawberry Valley" before it became known as "Sisson" which was sometime before 1900.
As for San Francisco, records before the 1906 earthquake are difficult to find. However, my father's family comes from Old San Francisco dating back into the 1860s so I have quite a bit of information in case you find that your relative was there. It is a good possibility I'd think as the other areas of California you mention were very remote (and still are today) during the time you mention but they were indeed Gold Rush country nonetheless. San Francisco was more or less a place that most gold miners went to or stayed at some point during their treks in and out of the mines.
I know that there is a California Birth Index available on ancestry.com. It may be useful for you, I cannot say. I don't have a subscription with them right now (giving it a break for awhile and waiting for a "deal" on a subscription hopefully at a later time).
Another odd thing we have in common is that odd place, Dunklin Country (aka "Boot Country") Missouri. I have many relatives from Kennett which is in Dunklin County. Kennett is pop. 18,000 today and it never had a large population and was known to be cotton picking land pre-1900 into the early 1900s.
My Missouri relatives are on my mother's side and many of them were mixed blood Indian folk (Cherokee, Choctaw and Chickasaw). Are you surprised yet? Many of these same people were from Tennessee, Arkansas, Mississippi and other nearby places as well as various parts of northern Texas.
I do have a lot of San Francisco records and the old newspapers can be found on-line - the SF Call from the late 1897 to 1910. Many parts of California can be found in these online indexes (scroll down and you'll see the San Francisco call below the Salt Lake herald (Utah.). You'll also see other old newspapers listed on this same link that have Jefferson, Texas on it, etc. :)
http://chroniclingamerica.loc.gov/search/pages/ Best of luck to you and let me know if I can be of more help in locating your ancestor that came to California. Given the time frame you have defined, I'd suspect he came overland to California.
CountAllVotes
:D