We went when DC were about that age and it was an amazing trip.
In San Francisco I'd definitely recommend going to Alcatraz - you need to book a long time in advance though.
San Francisco has sea lions in the Bay and you can have clam chowder in a sourdough loaf. You can rent bikes and cycle over the Golden Gate bridge (we didn't - not DD's thing) and of course there is Chinatown.
Parking is expensive in SF so we picked our car up after our 3 days there at the recommendation of our travel agent.
Then went to Yosemite for 3 nights and stayed in a wooden cabin which was a highlight of the trip. Amazing scenery. We saw a bear crossing the road and lots of fat squirrels. DS and DH climbed up beside a waterfall and had a dip. It's about a 4 hour drive to Yosemite however, the roads are twisty and DD was car sick!
As an alternative, friends camped in Big Sur which is down the coast road. Again lots of wildlife to see and amazing views.
Monterrey has an amazing Aquarium which DD loved, particularly the sea otters.
On the way down highway 1 there are various beaches to stop at, some with fat sea lions.
We didn't stop at Hearst Castle which I regret as friends have raved about it.
We did stop at Solvang though, which is made to look like an old timber Swiss type village but is actually modern concrete!
We stayed a couple of nights at Pismo Beach which is a little seaside place with a boardwalk and then another couple of nights in Santa Barbara which is more upmarket. Both ok but not amazing.
We then went to LA and stayed in Santa Monica for 4 nights which was fabulous. There is a fair at the end of the pier and it is accessible for Hollywood. I'd strongly recommend the Warner Bros tour and Hollywood walking tour. Also highly recommend going to an LA Dodgers baseball game also accessible from Santa Monica. We didn't do Disney but went to Universal Studios. Not great but I think its better now.
We actually had a 3 week trip so went on to Grand Canyon via Las Vegas before flying back from Phoenix but originally planned to fly back from LAX.
There are loads of other things to do in LA so if I had my time again I'd have spent more time there and less in Pismo and Santa Barbara.