Thanks for posting your query.
Removal of 3 molars causes difficulty in chewing not in swallowing.
There is least chances of difficulty in swallowing due to molar teeth pathology as the lesion is improving (as you have mentioned).
with pain in swallowing may be due to enlarged tonsils.
Cough and fever
occurs when upper respiratory tract
Tonsils is a part of adenoid
tissue (a collection of lymphoid tissue), which helps in preventing infectious agent to enter in our body.
Enlargement of tonsil indicates ingestion of microorganisms and doesn't always associated with fever and cough.
Dr. Mayank Bhargava