I am not sure what they are but I think you should see an oral surgeon for a definitive diagnosis and more appropriate medication.
How long has he had the spots? Usually mouth problems heal in about 7-10 days. Some of the mouth rinses like what we call "magic mouth wash" it has lidocaine in it which can be a numbing agent. I'm sorry for your little one in such pain. Motrin is better because it has anti-inflamatory in it. "magic mouth wash" has Benadryl, maylox, lidocaine, and I'm not sure what else, but if you are interested I could ask the dentist that I work for what the prescription is. Watch out for the things he eats and drinks no o.j., tomatoes, ketchup, etc. I hope he gets to feeling better!!