"your question seems to be how long would it take for your wife to not react to some unspecified component of the chicken manure, based on a reaction that is not described. Can you provide any other data?"
She learned that she has inflammatory muscle neuropathy. Basically think of MS and you'll get an idea of what it is. Some component in manure, dust of the coop, or whatever, made her lungs really inflamed and reduced her lung capacity severely. It is already compromised due to her muscle weakness. Once she stopped being around the chickens, the lung inflammation stopped. It is some kind of inflammatory reaction which is making her very sick so I am taking care of the chickens now and she just watches them from afar.