Nick,
So sorry that you are living through this nightmare...On my list would be a kink, a twist, a stricture, diverticulitis (can it occure in the small intestine?), a hernia and or a kidney problem....not that I wish any of the above on you....but those are what comes to mind.
Sharon

You did not say how long you have had your pouch. After I had mine for about 4 years, I started having pain and nausea on my left side. My concern was scar tissue. Scar tissues does not show up on any scans. After some tests, my GI doctor determined that I had some gallstones, but that they were not of a size or location that should be bothering me. He reluctantly sent me to a general surgeon to remove the gallstones and look for scar tissue. Low and behold there was scar tissue. He removed it and the pain was gone immediately. I do some occasional massage type exercises to hopefully keep this problem from coming back. That said; as Sharon said, it could be many other things. I hope you figure it out soon. Good luck.