With only two full days and three huge and very trafficky metro areas to navigate, frankly I'd skip the coastal option and just head to the desert, Palm Springs specifically. The drive from SAN to PS takes a couple of hours; I'd probably net even try to get anywhere on the Monday you land; the route crosses some mountains, and while wintery conditions are unlikely, after going through the border yoga at SAN it could well be getting dark by the time you're in the hills, not ideal.
There are several nonstop flights daily from PSP to SFO ($79 on UA) so what I'd do is take Tuesday and Wednesday to explore the Coachella Valley and especially Joshua Tree National Park, and maybe drive a little on old Route 66, then drop the car at PSP and fly up to SFO, arriving at or before you were planning to get there anyway.
Google the places on this map -
https://goo.gl/maps/y9Z3yEJhXZLx3pLM8 . These include the Palm Springs Aerial tramway, which will take you from the desert to (likely) snow up on Mt. San Jacinto. A loop through Joshua Tree is an easy and incredibly rewarding day's drive; maybe cap it off with a date milk shake at iconic Shield's Date Farm in Indio. You could also spend a day heading up to old Route 66 near the "town" of Amboy, just to say you've done it. Map -
https://goo.gl/maps/W6HPkMp1ZBX6aw966
There are numerous places to stay in Palm Springs, in all budget ranges. And the food options are also extensive; I'd highly recommend Sherman's in PS for a real Jewish deli experience, and there are fantastic Mexican cafes and restaurants up and down the valley. Palm Springs is home to terrific mid-century architecture, a very fine wee art museum, and lots of cool shops. For what it's worth, PS is also home to a very big and active gay community.
A couple of Joshua Tree pictures, taken in January a few years ago.
