Have been given a good report by an "ent"& an internist. I have thyroid disease (tk levo) & HPV (tk aldara). Why do I still have a chronic sore throat?

Combination of thing. A few thoughts- although you may not have had anything obvious on ENT exam you may still have subclinical gerd, post nasal drip, allergy or even irritant. I would review your hx to see if there is anything we are missing - try trials of appropriate meds including standard anti gerd, anti drip and anti allergy. At the end of the day this might be a combo of things.