K., This does sound like an allergy to the antibiotics. However, I would not wait until tomorrow only wait a few more hours and call the doctor again. If they say to wait until tomorrow, then tell them they are full of it and take your son to the emergency room. If he is not getting better and now has hives, something is going on and he needs to be tested right away. Doctors like to tell you to wait it out so that the child can develop an immunitiy to the sickness, but at 3, the immunity is already there to a point and if he is no better after being sick for 2 weeks, then something else has to be done. I would not wait longer than a few hours more. If he is not better get to an emergency room. To sooth the hives, you can try a little vasoline to help with the itching and it may even help them to go away. A warm bath with a extremely mild soap may help too. If you have an oatmeal bath from Aveeno that is really good too for skin hives and irritations. Good luck.
I have only one child also. I have lost all my other babies so she is special to me. I don't wait things out as long as they say to just because they say to. A few more hours should tell the tale for you.