This pond is designed for 5 to 8 adult koi. At 125 koi you may have 45 pounds of fish in the water based on what you have described. That water to pound ratio is about 50 gallons a pound at the moment, so your filter should be sized to handle that fish weight. So if your filter is large enough your enormous school should still be fine, and you are operating a vendor pond. Vendor ponds have specific data characteristics that differ from hybrid watergardens.. I’ve seen 4000 koi of this size in a vendor pond and they had no disease. Fish number does not kill fish. The only way you will know if there is a parasite is to scrape, clip and scope. Any analysis without microscope observation is invalid. Nitrate values are meaningless really. The definitive aquaculture study on nitrate showed no impact even at 600. If you measure temperature, ammonia, pH, nitrites, and water turbidity, that’s plenty of data. As for parasites, yours probably came from your vendor even though that person says they quarantined. Just because they say they quarantine, that doesn’t mean they were successful. One of our members brought in fish that had been quarantined twice and ended up with chidonella. Parasites do not fall from the sky. They must arrive on a live animal. That’s why they are parasites. Opportunistic bacteria do fall from the sky. Pseudomonas infest all seeds for example.
So you take all the fish out and treat the pond for parasites. Except for ick that forms a cyst on the sidewall and then releases tomites into the water to attack other fish, the parasites are on the fish. They can’t live more than about 20 minutes outside a fish body. Ick that has formed a cyst on the pond wall cannot be killed because they are in the cyst. You need to treat your fish if you are parasite hunting.
There is something else going on here and we do not have the required data. Part of the data is measurement. Another part is pond structural design. The third piece is fish behavior and condition, especially sick fish behavior. Surface gasping, pectoral tucking, disorientation, flashing except during feeding, visible wounds, fin or mouth damage, red lines in the fins, spiderwebbing, pineconing, and isolating all tell different stories. Tell us their stories since the story is incomplete at the moment.