My two cents ...
This is my experience while treating the Whirling disease. I had wild fishes in two tanks showing the symptoms. The interesting thing i noted is that at a time only one fish was showing the symptom. The first tank i lost two of them and then on checking with lot of folks I got the following suggestion. This was from a reputed breeder in Asia (I was told not to put his name anywhere ). He asked me to use tetracycline and Metronidazole. The dosage for both is 750 mg per 100 liters of water. In case the fishes still show the symptoms after 24 hrs of treatment increase the dosage to 1gm per 100 liters. As a last resort i tried it in both my tanks and since then for the last one month the fishes have not shown the symptoms. He specifically told me not to use light during the treatment. Also keep the temperature at 31 degrees. The treatment was suggested for 6 days and after 24 hrs do 25% water and dose the medicines appropriately. It worked for me. So in the worst case you may want to give it a try. Also he was suggesting that I should be treating all the fishes in the tank and not only the fish that was showing the symptoms.