I thought I would type some of what I have noticed, to see if it makes sense or provides any clues
California Death Index
J S Cole, born c1827 - your John?
Death: 25 September 1907, Humboldt
1907 Eureka Directory
John S. Cole, McFarlan avenue, No. 1433 - your John?
1900 Eureka Census
John S Cole, born April 1829, married 40 years, born England as were parents, immigrated 1862, naturalized
Mary Cole, wife, born November 1837, married 40 years, no children, born Ireland as were parents
Harrison Street address
Harrison Avenue is two blocks away from McFarlan Avenue - they run the same direction.
1896 Humboldt Voter Registration
John Silas Cole, Farmer, age 70, 5'8", dark complexion, hazel eyes, white hair, born England, naturalized April 7, 1873, Humboldt Co.
1888 Humboldt Voter Registration
John Silas Cole, Farmer, age 60, born England, naturalized (same info as above). Local residence: Bay
1880 Arcata, Humboldt Co Census
John S. Cole, age 50 (born c1830) England as were parents, Farmer
Mary B. Cole, age 45 (born c1835) Ireland as were parents
1873 Voter Register
John Silas Cole, age 43, born England, Farmer, Arcata, same naturalization info as above, plus 8th Jud Dist
1870 Eureka Census
John Cole, age 39, ? Labourer, born England
Mary Cole, age 37, H.K.?, born Ireland
According to the voter registers in San Francisco, your John was not (different naturalization date and place than your John):
John Cole, age 36, Harnessmaker, 632 Second (1866 record)
Not much help. The only thing that I see is that he liked to use his middle name or initial.