I usually do pulmocort then albuterol treatments with our son and it helps a great deal. What about his pulse ox? How is it? That says alot, have they ever tested for atalectsis of the lungs that will make them cough and can easily be confused for aspiration pneumonia. Also sometimes they will just cough to clear there throat, but every child is different our son was born with esophageal atresia down syndrome and tracheomalacia and bronchomalacia and laryngomalacia, so i can relate. I have a web site at kaylapearson.com. i hope this was of some help
also acid reflux, and allof the things above can make them cough so it is hard to sort out.