Hello and welcome to Share.
I am sorry that you are dealing with this! It sounds like you all are having a rough time.
Have you talked to your doctor about why they started prednisone? I am not sure what that medicine is for, perhaps now that he has been on it for months and his symptoms are getting worse, you can contact the doctor and ask about changing the medicine? Sometimes there are several medicines that do the same job, but some have way less side effects. Speak to the doctor and see what he or she thinks.
My son was born at 27 weeks, had a g tube, BPD, and a ton of gas. He was in pain a lot when he wasn't being vented like you mentioned. He also had a nissen procedure, so he could not vomit, so we did not deal with this exact issue.
Keep us posted, I hope you all figure something out soon!