What Causes Headache And Painful Neck?

Hi, I’m 20 years of age suffering with persistent headaches. I am roughly 5'6 and weigh 14st.10lbs. I had a severe headache about a week ago which felt like a stabbing pain and afterwards had a milder headache consisting of a throbbing pain daily for about a week. I also get a stiff and painful neck with this (especially if I turn or tilt my head back) and experience a slight shaking sensation. I furthermore have muscles that ache causing normal movements to sometimes be uncomfortable (shoulder blade, leg, knee, arm, back etc...) at different times and on occasions get muscle spasm. I also noticed how frequently my bones click if I sit up straight or stretch. I am consistently fatigued, feeling un-rested when waking up. I did get diagnosed with an underactive thyroid which I am currently being treated for and am aware that the tiredness could be due to this however I sometimes also flush hot (only on occasions.) My doctor believes that I suffer with migraines and gave me tablets for this but the medicine doesn’t stop any of the pain in my neck and the shaking continues. Is there something else that could be causing my problems?