Well, first off, I don't think you were overcleaning your tank. The uncycled method means you have to not only change the water, but clean the tank. The concept is based on providing your fish with a sterile environment with no beneficial bacteria and no ammonia.
Anyway, are the spots fuzzy? Perhaps lowering the temperature slowly by a degree every couple of hours will help stop the bacteria from growing. Some bacteria become extremely active at around 80 degrees, so slowly lowering the temperature to around 76 degrees can be quite helpful.
Can you describe any changes in behavior that you've observed? Lethargy, rapid breathing, clamped fins, hiding, darting, floating, sinking--that kind of thing--it can give us a better idea of how bad he's feeling and how severe the infection may be.