First of all let me congratulate you on keeping her well through this situation and for dealing the an extremely ill infant. It's tough! What I do want to say is I'm not qualified, as are few to give you the help you really need. But there is one place you might want to consider and it's a holistic specialist. Traditional medicine is wonderful at treating situations such as your daughters, but when it comes to nutrition, they aren't as good. We have a lot to learn about food, and from what I've discovered subtle food changes work miracles. My story is not mean to downplay your situation, but it may help. My dogs, yes I'm talking about my puppies, were having some serious problems. My first dog was diagnosed with Transition Cell Carcinoma about 3 months ago, and at this time I was told about some dietary switches that could help slow even reverse the process. These weren't weired changes such as using ground sea kelp during the full moon or anything; they were simple changes such as supplementing with yogurt. Guess what, they worked.
My next situation is my 9 week old puppy that we have bottle fed since he was 2 days old. He has had skin problems for about a month, and the Vet has tried everything. I finally turned to the holisitc side and changed his food to a holisic kind and added yogurt. Within one feeding things were better. I guess you can do some research on what natural foods could help her. When I read your posting I noticed that you were mentioning processed foods, which in themselves can cause problems. If she is not on immunosupression therapy, then you could try a more holistic approach using fresh foods, which may make a difference.
I hope this at least gives you a place to start looking; I used to make fun of my neighbor because of her organic food and her concious effort to eat only the right foods, but I'm slowly coming to her side. I've seen first hand the difference with a few small changes.