Cecil,
I am worried about the fin fungus contagion. If it is not contagious, how is it is that so many in the cage have it?
The ones that have it were the most easily stressed and/or had some issues with handling worse than the others did. Fungus is something that takes advantage of a compromise in the slime coating, superficial surface injuries, or it's a secondary infection due to bacterial issues. It's not uncommon in winter at all. In fact fungus prefers cold water. Once the water warms, the fish feed better, and their immune systems are up to par, many will snap out of it if they aren't covered too heavily with the fungus.
It's not contagious unless the fish suffer continued damage to their epithelial layer and the spores present have access to that skin damage. Most likely however the damage that was done initially by handling is no longer taking place.
Second question, how in the world can you treat fish in a cage where water flow exists?
The friend in Illinois mixes small amount in a container and spreads it on the surface of the cage. It quickly spreads out inside the cage via diffusion and does it's thing before being diluted by the water.
If you have any questions his name is Jeff Blankenship of A & J Fisheries in Vandalia, ILL (618) 780-3919. I'm sure he'd be happy to tell you. He's a super nice guy that likes to talk just like me. Only problem is when we talk it never ends.