Your profile doesn't indicate any meds that you are taking or if you have a diagnosis, so I am assuming that you are not yet diagnosed and the scope will be the first step in your process.
If it is crohn's, your pain could literally be anywhere from your mouth to your butt. Lower right abdominal is normally the first, but I certainly did get upper abdominal pain. I periodically still do. Turns out I have a hiatal hernia, and I do get pain from that. You may also have a build up or slow passage of bowel gasses. These can also cause pain, and can make your breathing more uncomfortable. Are you getting distended or bloated when you have difficulty breathing? Are you noticing a change in how you pass gas? Is it time of day or food related? While you are waiting for your scope, you may want to start keeping a food journal (what you eat, when you eat, approx amounts), and tracking what happens when you void your bowels. It could help your docs out a lot. Best wishes that your case is easily resolved.