I think you are doing a phenomenal job in managing a medically complex case. The one thing that does come to mind is perhaps consulting with a Registered Dietician for dietary recommendations. Also an Occupational Therapist could be beneficial on positioning of ventilation support during meal time. My thought would be to schedule several feedings/meals a day and particularly when the congestion seems to be less or after pulmonary toileting efforts.

Sorry @benwa1950 have absolutely no idea why, how, when the thought of possible parasites would come to mind?!