Throat Pain and Ears, help

So for about two weeks I've been having muscular aches in my throat and some ear pain and some headaches, I think this happened when I had an endoscopy for GERD two weeks ago after 2 days after the procedure I started getting extreme muscle type aches in my entire throat area it was horrible, I went to my doctor he doesn't think there's an infection since I had tonsilitis not to long ago, I'm starting to think it has something to do with my thyroid since the pain doesn't go away, right now i'm taking antibiotics and allergy medication also i'm a 19 year old male.