Having recently been a kid, still a kid, and having grown up in Norcal and gone to school down south, being the cool SoCal cousin to lots of kid cousins, I do this trip all the time:
San Diego: Unless you know your kids go crazy for zoos, I would go to the zoo the first day, see what you get done, including if you do the safari, and see how much your kids actually want to do the second day/ if there is anything you even missed. While you could spend a lot of time in the SD zoo, there is so much beauty in the area. For instance, instead of the zoo the second day I'd take them to the tide pools, where they can explore and see the animals there. Fleet Science Center is awesome.
Go to Disneyland on a week day if your schedule allows, no questions. You will get so much more bang for your buck. It's all awesome, the new Carsland is really well done, as is everything Disney. There's other stuff in LA, but I think Disney is the best for that age, especially if for only two days.
Sequioia/Yosemite- tough on the weather, too bad you weren't here this week! These would be worth their own trip. Alternative to this is if you go west route, Big Sur is awesome and of a similar vain. Sometimes the foggy weather is awesome for a short hike and to "get lost" in the big trees.
If going the west route, Monterey/ Santa Cruz is awesome. Any beaches in that area are super fun. You could do a picnic day at Asilomar and go look at the tide pools, buy a kite and go to Seaside and watch the paragliders and walk the beach. The water will be cold, but there so much to do at both just enjoying the ocean. Much of my childhood was spent running around on those beaches. MONTEREY BAY AQUARIUM, it's the best. You could rent a quad bicycle and bike along the coast as well (we usually couple the aquarium and this in the same day, as they are both near each other, same parking spot. Also, if you and your kids like cars (6 year old might), Laguna Seca is right there, always track day or something going to stop by and watch.
SF-- You could spend all of it here as well. As a kid centric vacation, I'd recommend the new Exploratorium (half a day) Cal Academy of Science, Chinatown(must do for dinner and walk into all the trinket shops, if you want a dinner recommendation let me know). Since you have a car, if it's a semi clear night, drive on the bridge to treasure island (get off on treasure island) and there's a parking lot right there, you will have the best view of the city sans being on a boat.
If you're there on a weekday, go to Pier 39 for the merry goround and to see the Pier, it's a tourist trap so avoid on the weekends. If you have time the kids would also love Alcatraz, and it's a short enough ferry for the kids to not be too bad. Walk some of the Golden Gate if your kids are walkers. These lists could go on, and on....