I second Nature Aquarium. The store is beautiful. Most tanks are beautifully scaped. They buy their tanks and stuff from AFA as far as I know. It's in Santa Monica near 3rd street Promenade if you so choose to visit. I bought both my 60H and 60P from Toru.
I'd add Seaside Tropical Fish in Huntington Beach. Despite their name, I'd say their specialty is marine fish that takes up 3/4 of the store. The store is very pretty. It's also close to HB downtown if you choose to visit.
Most of the other stores on your list that I can recognize is not worth seeing in my opinion such as 405 and Tongs. Nice stores but pretty generic and not worth the drive. But, that's me. Oh, and they are in OC not SD.