Sores and fungus on your fish are not directly due to clear water. The fish's health problems are probably due to being too crowded and the resultant lack of food in the ecosystem. Indirectly clear water results in less food. Although you can still get into your dying fish situation if you increase the food resources and then the fish numbers ultimately also increase without some sort of a harvest or population adjustment. As is preached here often, Ponds, have carrying capacities or limits as to how many fish they will raise. Fisheries need to be eventually thinnned or Mother Nature does the thinning and you usually do like the way she does it; as in your and Cecil's (above) examples.
Also did youcheck for the fat content of your dying fish?
