In your daughter's case we need to know whether proper diagnosis of hypothyroidism was established or not. It is also important to know whether this dose of Eltroxin is adequate or not. Weight loss and leg pains can occur if there is overdose of thyroxin. Best way to know this will be to do TSH now. If normal then this dose is ok for her but if low this suggests that her requirements are less or not at all. I would suggest you to provide the first report of TSH at the time of diagnosis and one recent one. Other common cause of body aches and pains is vitamin D deficiency and reduced calcium intake (milk). Other diseases, which needs to be ruled out is cortisol deficiency and some intestinal problem. Cortisol is a hormone released from adrenal glands located just above kidneys. Hypothyoidism and cortisol deficiency can co-exist. She needs a detailed evaluation from a child specialist.