We have since learned that this is something he can and probably will outgrow. In the meantime we are being faithful at giving him his pump four times a day, his prednisone (a steroid), and Mark even spent a couple hours yesterday washing down the walls in his room, vacuuming, mopping the floors, and airing it out. It was a relatively mild day yesterday so he opened his window and let in some fresh air for awhile. The next step for me is to study up a bit on how diet can affect stuff for him and to see what kind of foods to avoid for a time.
update: The treatments are done for the time being. I tried to make an appointment with J's pediatrician and can't get in to see her until May 26th!! He has virtually stopped all nighttime coughing, so we are hopeful.