I would also think in addition to having you do nebs and CPT that at the very leasat they'd to a fecal fat test to determine if he's pancreatic insufficient. Simple test where they test a stool sample and determine if he needs digestive enzymes. Has he been tested for RSV, have they done any sputum samples/throat cultures to determine if/what bugs he's growing.
DS had a horrible cough at 2 months, so bad that I'd have to hold him over sinks because he'd throw up his formula. We were already doing CPT with albuterol/atrovent nebs 4 times a day, he was on keflex (antibiotic as well). Turned out he had enterbactor cholae which caused bronchitis and needed yet another oral antibiotic.