Welcome in H.C.M.
I had carefully considered all aspects of your symptoms and it appears as you are having chronic tonsillitis
with recurrent pharyngitis
As your tonsils are appearing as chronically inflamed and they are the site for spreading infection in throat from time to time. Once the throat gets infected you feel lot of pain in swallowing and there is cough also along with fever and malaise
I would like to suggest you for-
1- Culture and sensitivity of throat swab.
2- Sputum for AFB & gram's stain.
3- X-Ray chest & paranasal sinuses
4- Blood- CBC, ESR, blood sugar (F & PP).
By the inferences of above investigations and their co-relation with clinical findings one can make diagnosis that can be manage accordingly.