Viruses may last for about 2 weeks in kids.
It might be a fresh infection if he was completely okay in between.
Pain in his ears may be because of fluid collection in his middle ear- that often happens in kids with upper respiratory infection
Its better that you have him seen by your Pediatrician- as he might need decongestants and anti-histamines too along with fever
Give him plenty of fluids in his diet (Vegetable soups, milk, porridge, plain water).
Hope my answer helps you.
Wish your son a speedy recovery.