It sounds like a viral rash to me. These are very common after viruses, especially ones with fever and generally are nothing to worry about. Just keep an eye on him and if he acts like he is feeling better, then he is probably fine and the rash will clear on its own.
My son wouold break out like that every 6 mo and it was like hives. It has not happened for a while. I remember the last was the scariest at 2 yrs old. He had a very high fever 105 and I rushed to the ER.Viral or something they did not know, they said it could be an alergic reaction to something. Steroids and ibprophen. He was ok.
If the spots look like blisters its Chicken Pox try not to let him scratch as they leave marks, it could also be Measles , give him plenty of rest and fluid take him back to the Doc if he gets worse.