sounds similar to my son. I just posted on the recurring fevers forum but I mention in there that he had to get grommets. They were for the ongoing infections after the hospital and even after the immune isolation period. Your sons symptoms sound very similar to how my son was with ear infections and I had to tell my GP that I wanted a referral to a specialist. The specialist put grommets in 3 days after first seeing him and couldn't believe that he hadn't been referred earlier. The use of antibiotics covers up a lot of stuff and it clears the infection temporarily so that it slowly creeps back again, usually the throat is a little red and the nose a little bit runny but not much else then the next thing you know you have a full scale temperature and full on ear infection.

I do not see how you can tell if something is bacterial or viral, or that it changes to such after a few days. Antibiotics only help bacterial infections, so if it is viral only, then it is going to come back. There are various reasons for fever other than colds.

What you could try also besides taking him to the doctor (since that obviously isn't working) is to give him Elderberry Syrup or extract, which is known for it's ability to combat viruses effectively.