...the lungs.
Here is something recommended by doctors to help the recovery of the function of the lungs:
Deep breath exercise: take deep breath through the nose for two seconds, fill the lungs so both the chest and the stomach rise, then let out the air through the mouth. Do these eight to ten times. Repeat each hour. (it could be a little difficult to start with, particularly if coughing also, but one will get used to it). This exercise could be quite important to help reduce/eliminate permanent damage to the lungs.
Regarding sleeping, try different positions: sides or face down on the stomach. The face down position seems to be very helpful for more comfortable sleeping for many.
Hope you a speedy and full recovery!