This route might work for you. It does have some climbing but a lot of it is on low traffic rural roads. From Yosemite take 140 through Mariposa. After Mariposa take a right on J16 (Hornitos rd). Follow this through Hornitos and Merced Falls until you get to Snelling. Then take 59 until J17 (Turlock Rd.) Take J17 to Patterson and the I5. Go under I5 and take a right on Del Puerto Canyon Rd. (130). This becomes San Antonio Valley Rd and will take you into San Jose. At this point there are some bike maps that should get you to SF. A local may be able to give you the best route up to SF.