If your bird is getting over fowl pox, which is a virus, she as a lowered immune system which can cause many different problems. Fungal infections are possible with a lowered immune system. There are contaminants EVERYWHERE no matter what you do. Mulch, peanuts, wet litter, moldy food, wet nesting material, unwashed veggies/fruits, corn just to name a few. Fungal infections as well as viruses can show their ugliness in the form of respiratory problems sometimes. Treating with respiratory drugs will not help, sometimes making it worse. Instead of trying all the respiratory drugs available, maybe look into an anti-fungal. Unfortunately, I think they are only available from a vet.
Other than that, all I can say is treat her for a virus. Clean (with bleach) her food and water bowl EVERYDAY. Give fresh water and fresh food EVERYDAY. You can even change the water twice a day. Many germs/organisms get deposited into the water and food bowl all day as the bird eats and drink, this is a very quick and popular way to spread an illness. Look in to a good daily vitamin, aviacharge 2000 is wonderful and easy to purchase over the internet. Feed only good quality feed, no corn (unless given sparingly as a treat once in a while). Up the protien using scrambled eggs if needed. Wishing you a full recovery.