i *think* i recently read that armour has changed their formulation. you want to find a brand of thyroid that has all the T leg -- t1, t2, t3, and t4.
i can't remember if armour is porcine or bovine, but the source can also make a difference if you are allergic... which in your case it doesn't sound like what is going on.
in any case, you reaction is obviously not what is supposed to happen when you take thyroid hormone, unless you are undergoing a massive detoxification.
have you had a hair test for metals toxicity? i suggest using andrew cutler's counting rules method for mineral ratios.
is it an option for you to discontinue the meds right now or at least back off significantly on the dose?