I have been taking Levothyroxine since 1999. The aches and soreness does seem to increase if I do the least bit of work. And if I do alot of work, like work in the flower bed I am just about past going the next day.
Those are very common symptoms of Hyperthyroidism , you need to lower you Levothyroxine dose , i also suggest to discuss your doctor to prescribe you brand medicine for thyroid like Levoxyl or Synthyroid which has less filler as compare to generic one. How long have you been in thyroid condition. Does your muscles aches and soreness started after doing little but of work ?