I can’t much to the logistics of your trip. You have gotten great advice, but don’t skip the San Diego Zoo.

A few things from a San Diegan with two small children...

Flights from LAX to SAN can be really hectic and you'll have to switch terminals. Living in San Diego, we would rather drive. If you do the drive in the evening after 7pm, it is usually 2 - 2.5 hours. Your morning traffic will be a bit worse, but if you leave mid morning, like 9am, you'll miss the morning rush. There's always a chance in LA... but that's kind of traveling in general.

For your San Diego itinerary, I love that you're including the San Diego Model Railroad Museum (where I work). We have toy train room that is really popular with the kids and families love it. Our hours may be expanding for the summer, but we're currently open Thursday - Sunday. There's a lot of other wonderful museums in Balboa Park that kids of that age will love including the Fleet Science Center, The Nat, The Air & Space Museum, etc. The Balboa Park Explorer Pass is a great way to see a few museums at one price so you don't feel bad if the kids whiz through one.

Other things to do in San Diego with the kids would include the Waterfront Park downtown, and they might get a kick out of the Midway (air craft carrier) Museum. That is also where the whale watching cruises leave from, but with kids, I would consider the Seal Tours or the Harbor Cruise instead.

Old Town isn't my first choice for an entire day, but its a great place to get dinner one night and wander around a bit. Presidio Park on the top of the hill has great views and the Serra Museum. Whaley House is a Haunted House museum which can also be fun.

As locals, we go to Liberty Station a lot. It has a lot of good places to eat like the Stone Brewery (huge event center and outside eating options), parks, art, music, shopping, etc.

I don't think Escondido is going to be worth the drive. It's not far, but we usually go to Safari Park and that area because we've exhausted local options. The San Diego Zoo is amazing and they've just opened up their Children's zoo area. Don't forget about SeaWorld which is also fun. They just opened Sesame Place which is a water park a bit further south. Some of their passes can combine visits to both.

I would consider some of the San Diego Mission Bay properties in addition to Pacific Beach. They'll be easier to get to all that you want to do, and I don't even see a PB beach day on your itinerary though it is reasonably close to La Jolla. Usually a more central (and economical) option would be to check out Mission Valley. The Town and Country Resort just finished a massive renovation and might have some good rates with the pools and things you want.

Los Angeles... I would add in the Griffith Observatory and I hear the Tar Pits are cool though I have never been. Disneyland - plan for 2 full days, one at each park. Depending on hotel rates, a 3rd hotel night might be in order. If you get something close, we have always started early, gone to the hotel for a nap, and then back to the park for the rest of the evening.

I agree that the Sequoias may be for another trip. Southern California has some great local mountains including Lake Arrowhead, Big Bear Lake, and Idyllwild. Bear in mind that September is going to be hot still and many of the accommodates will not offer AC. Big Bear looks like its the coolest when looking at average September temps. The wildfire season can start early though... the really big ones we've had in the last 20 years in San Diego have been early October. Overall, it is a very dry and dusty part of the year. I would suggest beach camping, but having just booked at Carlsbad in October, everything books exactly at the 6 month mark so your options will be pretty limited. Sometimes middle of the week spots can be available. You can also have trailers delivered to reduce your hassle. But all this still feels like a whole separate trip.

Hopefully these tips help. Good luck and I hope you have a wonderful trip!