J.C.
It does sound really familiar (my younger son, who is now 5.) I don't really have any advice although I agree that you may find as he gets older that a nighttime antihistimine like Benedryl might help because allergies might be part of the issue. Also, a vaporizer at night will help with the irritation and coughing now.
We went through that annoying cough thing for my son's whole first year - always taking him to the ped. only to find out it was just post-nasal drip/mucus, although it sounded awful. Good luck!