I had something like this when I was around 14. I had a really case of swine flu and the muscle aches and pain just never went away. Doctors had no idea what was wrong until I got an appointment with a specialist.
Apparently, the flu fried my nerves and gave me longterm symptoms of severe flu even though the virus was dead. Unfortunately the 'cure' was just to suffer until your body fixed itself, it took me around 18 months to recover fully.
Not sure if that's what you've got OP, but if so that sucks and you've got a long journey of pain ahead of you.