Ah yes, the good old Hand, Foot and Mouth fun and games, otherwise experienced in this house as Herpangina virus. There isn't anything more sucky than your little sweetie being in so much pain and not able to eat or drink.
The Benadryl and Maalox, aka "Magic Mouthwash" is pretty much your godsend now, along with Motrin and Tylenol. I would assume your son is running a fever as well? It's tough to get anything near their mouths when this virus is in its most acute stage. You might want to try ice cubes or ice cream, or something to help numb the area.
It just takes time, getting past this stage. It definitely sucks, but it will pass.
Good luck!
E.