You could drive to Disney and Universal from SD and make it back at night, but you'd be better off just finding a room in Orange County or LA for those days. You're looking at around 2 hours to Disneyland (depending on where in SD you are and traffic) and 3ish to Universal. Not out of the question to make that drive, though, just be prepared to face SoCal traffic which can extend those times by hours.
If you wanted to do a quick tour of SF you could easily see it in a day, but I suggest that you take 2 days there. It's a cool town and there's a lot to do.