Generally disease like that in a tank is a sign of water quality problems. So put sick fish into a hospital tank and then start working on your main tank. Check your filters are all working (don't over-vigorously clean them out as they will make your tank cycle again ie. you'll get ammonia and nitrite). The colour of your water is simply a cosmetic issue at the moment - get everyone healthy and then worry about what it looks like.
I'm assuming your tank is cycled - do check for ammonia and nitrite and if you find any do a 20% water change immediately and daily after that until they come down. If you tank was cycled before and now you're getting problems its possible the medicine has knocked out your beneficial bacteria. Also test your nitrate levels as very high levels can harm fish.
Fungus can be a symptom of too low temperatures, so put the temperature of your tank up to 80F and keep an eye on it, especially in the night.
Check any bogwood for signs of rot and do a gravel clean under rocks etc. to ensure no "dead spots" of anaerobic bacteria that could be poisoning your fish.
Then keep up a regime of frequent partial water changes and check your water parameters regularly. Have you been trying to alter pH or anything? pH swings can kill fish really easily, so don't use pH buffers etc. and if you have used them, allow the chemicals to be removed from the water with water changes.
Don't replace any fish until you've had healthy fish for at least a month. It is possible that whatever caused the fungus in the first place has affected their immune system so it may be you cannot save them. OTOH, some fish can be tough. Try Melafix in the main tank as that is a good tonic to cover fish with depleted immune systems. Also give your fish top quality food - live food, fresh food for the herbivores and frozen food.
I have had an experience not dissimilar to this - I had multiple problems in my tank, including filthy gravel and an unstable pH. But I saved most of my fish in the end.
