^That's a great time to visit San Diego for beach weather. June gloom should be over, and the water as warm as it gets.
Regarding the beaches, you can visit one after another with little problem during the week or early on the weekend. Some of the more popular areas stack up with traffic and parking can be a problem.
You'll find lots of touristy shopping at Seaport Village on San Diego Bay
http://www.seaportvillage.com/. The Embarcadero is just north of Seaport Village, the Midway aircraft carrier museum and the cruise ship terminal. Since you plan to visit La Jolla, you might stroll around the shops in the village. There are some high end places.
If I were to hit the highlights of San Diego's beach scene, here's where I'd go:
*Coronado's Strand, wide open sand, the beautiful Hotel Del
* Cabrillo Monument out on the tip of Pt Loma. Beautiful views, tide pools, and an historic lighthouse.
*From there I'd take the scenic drive along Sunset Cliffs to Mission Beach and Mission Bay. Mission Bay is a sparkling jewel fringed by parklands. Visit virtually anywhere but Fiesta Island's sandy wasteland. The western most areas such as Mariner's Cove and Bonita Cove and Vacation Isle are generally the nicest. You'll find Belmont Park and the historic Giant Dipper roller coaster at the foot of West Mission Bay Drive. Think touristy beach-side carnival.
*La Jolla - you can take surface streets from Mission Bay into La Jolla. That enclave is slow to navigate however you drive. Explore the point and Scripps Cove north of the Childrens' Pool, and also consider continuing just a bit farther north to La Jolla Shores for the mildest surf our coast has to offer.
*Bonus beach - north of La Jolla you'll find Torrey Pines State Park. You can stroll the quiet beach beneath the bluffs, or continue on into the state park for a series of easy hikes featuring gorgeous views.
Depending on how you spend your time, this could easily take more than a day or as little as half a day if you spend most of it in the car.
ComicCon should only impact the area immediately around the San Diego Convention Center.
I hope that helps. Enjoy your visit! We spend a lot of time on and around the water - we're feel lucky to live here.