Before even considering your question, I think we need to have a look at your thyroid related test results and reference ranges shown on the last few sets of your lab reports. Also please tell us about your symptoms.
Can you please post your current thyroid hormone levels? Be sure to include the corresponding reference ranges from the lab report, as ranges vary from lab to lab and have to come from your own report.
Do you know if you have Hashimoto's or not? Hashimoto's is the # 1 cause of hypothyroidism in the developed world. It's an autoimmune condition that, ultimately, destroys the thyroid.
While I would dispute the idea that the whey protein destroyed your thyroid, I would suggest that you should not use soy products, since they are goitrogens, which interfere with thyroid function. Also, protein is necessary for building muscle, but I learned from my own experience that there is such a thing as getting too much protein...
It would be most helpful if we could first see your current labs and reference ranges. We can go from there.
I don't understand what you mean that you weren't diagnosed as positive with Hashimoto's "for sure"... the diagnosis is simply a matter of having the antibody tests and you either have the antibodies or you don't...
Can you get copies of your labs? We've had a lot of members on the forum from Australia and none of them have ever had difficulty getting copies of their labs to post here for us, so we could see what their levels were. It's almost impossible to help if we don't know your actual levels and the reference ranges used by your lab.