Respiratory problems need answer?

My 3 month old son gets really rattly after he eats a bottle. He also coughs and chokes after the bottle. He has also had pyloric stenosis surgrey and the doctors had some problems getting him intubated before surgrey. He had RSV at 3 weeks old and was hospitalized, and now after his surgrey he has had respiratory disstress like every 2 weeks. When we go to the hospital they say it sounds like its a rattle in his upper airway like he is aspirating his bottles. So they did the barium swallow and thickend his feeds because they found he is at increase risk for aspiration. He is still having to go to the hospital every 2 weeks due to respiratory disstress and he had pnemonia the one time we went to the hospital. Why is he having so much respiratory disstress?? Do you think it is because he might have a intubation injury during surgrey or do you think it is abnormal sturcturing of his airways? I need some advice.