Excerpt from the book Running On Empty by Robyn Koumourou:
"It is not uncommon to start thyroid hormone therapy and find that your symptoms become worse before they get better. When you begin taking thyroxine the areas in the brain that control thyroid hormone production sense the increase in T4 levels within the blood stream. This feedback system will then cause the thyroid glands natural production of thyroid hormones to slow down.
Less natural T4 and T3 will then be produced and released and blood levels may remain stagnant or even decrease temporarily. Less free T3 hormone available to the body will slow down cellular metabolism. The symptoms of hypothyroidism may become worse until an increase in thyroxine is taken or an optimal dose is found."
What are your actual thyroid hormone levels? Please post the results of your most current labs, and be sure to include reference ranges, which vary lab to lab and have to come from your own report.
Additionally, since you've had several episodes of kidney stones, your calcium should be checked periodically, along with your vitamin D and PTH. If you've had those done, please post those results, as well.
It's true that symptoms often get worse or new ones begin, once one is on a thyroid replacement hormone. It takes 4-6 weeks for the med to reach full potential.