That sounds a little similar to a strange allergy that I've had since I was about 6 years old. I still have problems occasionally, but unfortunately we've never figured out what it is!!
I would wake up with spots/itching on, say, my writs/elbows. And it might get worse through the day. Then the next day I'd wake up and they might be all over my legs. It would last several days, and I'd have to take Benadryl. After a few days it would just go away. I think it would happen a few times a year, and I think it seemed to happen when the seasons changed. Just in the last few years I discovered that it seemed to help if I kept myself warm when the hives started. Maybe you could try that with your son.
I've been to an allergist to be tested and still don't know what it is. She did tell me though that it probably isn't a food allergy because a food allergy wouldn't cause hives for several days in a row like that & then just go away.
If you can, I would try taking your son to an allergist to see what they think, and possibly test him.
There are soooo many things we can be allergic to, from food to things in the air, to the cold!! (Yes, you can be allergic to cold temperatures, which I thought might have been my problem! It's called cold urticaria.)