A.R.
I hate to say this; but have you thought about it being Hand, Foot & Mouth disease? It is very common and can sometimes flair up only in the throat (making it harder to detect). This happened to my daughter at about 18 mos. old. She had no sores on the outside of her mouth, her hands or her feet. She (and then I) only had the sores in her throat, which made eating very painful. If that is what it is, there's not much you can do as far as treatment because it is a virus. It will eventually go away on it's own. Good luck!
A.