Riddle me this

Hana has been having an allergic reaction for the past week. It has literally made us sick to our stomachs to see her suffer- she scratches constantly, her belly and under her paws look as if she has been burned and her hair is falling out. I have never had a 9 month old puppy with these kind of issues so it has been both frightening and frustrating.
We took her to the vet on Thurs. and they suggested she might have a food allergy- we don't suspect environment because she never chews on her paws so it seems to be coming from within. She did receive antibiotics because she has scratched and chewed on herself so much it had become infected. The idea was to put her on hypoallergenic dog food which costs a mint and contains soy - soy is one of the top three allergens so I don't understand this and her food is already wheat free; wheat being one of the other top allergens. Luckily she takes her antibiotic with no problem but it did nothing to help the itching and I wanted this relief for her more than anything and so she would not need to continue scratching to the point of infection.
Finally we went to our favorite natural dog food store to ask for help and they suggested switching her to a fish diet and using an oatmeal shampoo to soothe the itching. So far the shampoo seems to have calmed the itching, now it is once an hour as opposed to every two minutes and I have not seen as many clumps of hair coming out.
However the biggest discovery I have made is that the flea product we used could be the culprit of this allergic reaction. This is very scary to find- there are literally hundreds of stories on the Internet describing the same thing that happened to Hana after I had given her this flea treatment- and I looked for similar stories on the flea treatment we used to give her and found very few. We won't know for a month if this is in fact the problem, but I really hope it is just so we have an answer and she suffers no more. It is so upsetting to watch her discomfort and I just want it to be over. Keep your fingers crossed that we can find out for sure what caused this so it does not happen again because I for one cannot take it!