Like others have said, post nasal drip could very likely be the cause. I developed this same issue after a horrendous sinus infection several months ago that had to be treated with antibiotics and steroids, even had to be scoped by ENT and was found to have reactive air way. (that is totally different than the clearing of throat, so don't go there with your son). I had not had anything like this before the sinus infection and I have never been the same since.
Because the post nasal drip has become an issue with my "voice box" due to thickness and increased amount of drainage, I have to clear more frequently.
My DR. told me to get a humidifier for my bedroom and turn it on about an hour before bed to get the room more humidified before sleeping, then leave it on all night. (Even if your furnace has a humidifier, it is not enough moisture in your house.)
Winter weather dries the atmosphere so much and secretions get stickier and thicker.
You might look into seeing if Mucinex would help him. Sudafed is very drying and it can keep one from sleeping, I would stay away from that with a child.