Headaches And Cracking Neck

I am 16 years old and have been living miserably for two years now. Starting when I was about 11, I began cracking or popping my neck several times per day and continued this for a few years. When I was 14, I began to get stiffness and pain in my neck along with headaches that seemed to be at the base of my skull. Eventually I had pain and headaches for every waking hour and could not concentrate at school. My neck is very stiff in the morning but the pain continues throughout the day, near the base of the skull. I also have a constant feeling of carsickness and dizziness, and this happens a lot when doing schoolwork. I don't pop my neck anymore for about a year and have gone through physical therapy. This helped somewhat but I am still suffering every minute of the day and the headaches and stiffness persist. I think I have messed up something bad, but an mri and x-ray showed nothing. Please, if anybody knows anything about this, please reply, as I am a very sad person to be experiencing this so early on in life especially since I am healthy otherwise.