Bit late, but this list by the user red river hog should be pretty comprehensive though it is missing a few species, and some species have been removed
San Diego Zoo Species List 7/29/22 [San Diego Zoo].
This list by the user Coelacanth18 is also very complete
San Diego Zoo Species List - May 2022 [San Diego Zoo].
The zoo does not keep as many fish species as other zoos, perhaps due to its proximity to Seaworld and the Birch Aquarium?
From the species lists above.
Koi are kept in a lagoon.
The acacia aviary has a tank that probably still holds Congo Tetra, Cuckoo Catfish, Duboisi Cichlid, Lemon Cichlid, and Leopard Bush Fish.
The hummingbird aviary has a pond stocked with feeder fish especially livebearers such as platy and perhaps guppy or mosquitofish? There may be cichlids in here as well, I did not get a good look.
The Wildlife Explorers Basecamp complex currently holds Giant Danio, Mchenga conophoros, Pinktail Chalceus, threadfin acara, blue acara, and freshwater angelfish in a tank which usually also holds a South American lungfish I believe, though the lungfish has not been on display for a while this year. There may be one or more other species in this tank.
Bluegills are kept outdoors with some turtles.
A sucker species of the family Catostomidae was in the Chinese giant salamander tank, likely as a feeder.
In the reptile exhibits fathead minnows and neon rainbowfish are mentioned in the list above but I do not remember seeing them. The minnows may also serve as feeders.
A large number of cichlids of various species are kept in the gharial pond. I saw a great blue heron hunting them and saw it pull out a fish that wasn't a cichlid, I'll try and get an id if possible since the photo was subpar.
Rosy Barb, Chinese Algae Eater, Green Scat, Giant Danio, and Banded Archerfish are kept in the Owens aviary.
Elephant Odyssey might still have western mosquito fish.
African cichlids are kept in a large amount of exhibits, the Sulfurhead aulonocara are kept in or next to the pygmy hippo and slender-snouted crocodile exhibit or in a separate tank that is next to them. Other species including the ones in the article you mentioned are from my memory, in the cool critters dwarf caiman and dwarf crocodile exhibits, hippo exhibit, and the dwarf crocodile exhibit in Africa Rocks plus maybe some that I missed.
All fish in the penguin exhibit, Blacksmith, Halfmoon, Leopard Shark, and Opaleye are off display seemingly permanently since the penguins were picking on them. The exhibit once held giant kelpfish years ago.
