Sounds like you have a solid plan. How many kids and how old? I would suggest exactly what you listed for kids. Plus Coronado is great - there's an area on Coronado with great views across the bay back into downtown. Then the ocean side of Coronado has the Hotel Del Coronado plus a long stretch of great beaches.
When you go to the zoo, leave a little while (even if just 30 minutes) to walk around the museums at Balboa Park (about 1/4 mile from the zoo entrance). Beautiful buildings, gardens, fountains,etc.
Also while you go to the USS Midway, alot a little time to walk along the bay there - great spot.
Also allow time to go to downtown La Jolla and do the 'coast walk' - a trail follows along the rocky coast with cliffs, where all the seals hang out. It smells like sh!t (literally), but it's a great spot.
If you're into golf you gotta see Torrey Pines. It's right on the coast on top of cliffs that are 200-300 feet over the beach. There's a hang glider port on the south side and a state park with walking trails on the north side.
Oh, one last thing: It can be cool here in June, even July. Our hot months are August and September. June and July are usually pretty hot & sunny if you go inland a few miles (80s and 90s just 5-10 miles inland), but along the coast it can be breezy and chilly (70s day, 60s night), often overcast. So bring jackets/windbreakers.