Flowerbud- when my son was about that age (3 1/2) he complained to me that his penis was ouchie. I did a check (he was working on retractability) and I discovered two raw spots, one on the foreskin and another on the corresponding surface of his glans. These spots were about 3mm across- small. It was obvious that he had torn an adhesion. How I don't know. the raw spots were not bleeding, it just looked pinker and raw. I put a dab of neosporin on it, and he said that tickled... so obviously the pain was not that bad- the adhesion was probably ready to go, like a really loose tooth. I put neosporin on the spot the next day and the third day there was no evidence of the raw at all.
So anyway- that was our experience. You might want to avoid neosporin if you have any doubts if he might have yeast infection because that would be bad for yeast. I doubt that my son needed any sort of medicating... it's just that he has come to expect a certain potocol with ouchies and the more steps involved and he moe colorful th bandids, the more comforted he feels.
Have you been to the Dr? Do you have an update?