I am suffering frm really bad headaches, tired all the time, pain in right knee, neck and right upper side. feel really low in myself.what could be wrong?

Sounds like: You are depressed. When you are depressed and down on yourself it makes everything in your body hurt too sometimes, and what is hurting hurt worse. I bet if you find a good counselor to work with you and your doc you will have less pain, deal better with your pains and start to really feel better inside too . When you can, exercise will be important!

May be fatigue: Since you have a history of taking levothyroxin, it may be time to have your thyroid checked. They can do a panel to see if it's low. I'm also you may benefit from seeing an osteopathic physician, who could do a complete musculoskeletal examination. They can examine you from the spine hips pelvis sacrum lower and upper extremities and ribs to determine what areas may be out of alignment.