It seems from the history that your son is having headache and he has taken doxycycline for about 2 years.
Doxycycline is known to headache as a result of idiopathic intracranial hypertension
caused by it. Since CT scan
have come normal need to rule out idiopathic intracranial hypertension as a cause for headache.
Hence I advice you to consult physician or preferably a neurologist
for examination and treatment accordingly.