Cloudy eye can happen if a fish's eye is injured (such as being bashed against a rock) and is healing. It can also happen because of a spike in toxins in the water (ammonia, for example). I also have two fish that just have and odd foggy look to their eyes--each one was that way when I bought them and it has never changed.
Can you get a nitrate test? They don't sell the nitrate test with the API pond kit--you have to get the aquarium kit for that test (or buy it separately). It's unusual to get high nitrates in a pond because of algae, but I still think it's worth testing.
Search hard for the body of the koi. If they are sitting in the water rotting, they could be exposing the remaining fish to more bacteria and toxins.
It's definitely hard to say what happened here. While the koi may have been carrying a disease and you should definitely quarantine new fish, I'm hesitant to say that's the extent of the problem. There are some diseases that can kill off huge numbers of fish, but usually only when the ecosystem is unsuitable for some reason.
For the record, I doubt pimafix or melafix would have handled the problem. Melafix is a disinfectant that can promote would healing and regrowth, but goldfish are so tough to begin with I am skeptical anything Melafix could handle would be a threat to a healthy goldfish.
In the future, I would be careful treating an entire pond with anything anti-bacterial, even something as milquetoast as Melafix. Here's why. You know how ladies can be at risk for yeast infection when taking antibiotics? This is because there is natural bacteria that on the body that out-compete or kill fungus. The antibiotics kill this bacteria off, and suddenly there's nothing to hold the yeast at bay. The same thing can happen in a pond. By treating a pond with anything antibacterial, you risk killing off benign bacteria or bacteria that the fish are well adapted to fighting off and opening up the playing field for other pathogens to move in.
You don't happen to have a microscope laying around, do you? There are some Protista species very commonly found in ponds that, while typically benign, can go berserk under the correct conditions. They cause scale loss, ulcers on the skin, ripped/torn/shredded fins. Secondary fungal infections could easily move in--and it kills fast. A wild animal could have brought in a parasite like that as easily as the new koi you got. Anyway, if you have a microscope, you can take a scraping of the goldfish's slime coat and take a look at it under the microscope. If you find creepy crawlies, then you will know you have a parasite problem.
Some other things that could go wrong:
- Algae blooms or major die-offs can affect the oxygenation.
- Decaying mater can create pockets of toxins that can be released into the pond if disturbed, poisoning fish (this is why you really need to look for those koi. If they're dead, you want their bodies out of the water).
- Water quality swings and fluctuations can cause problems. For example, a dramatic change in pH, or nirate levels.
- Runoff from rain storms can bring toxins/fertilizers, weird stuff into the water.
How are those tadpoles doing, by the way?
