It does sound like obstruction/adhesion pain. If it is adhesions, then a CT/MRI scan can't easily visualise them, which is probably why they never show up on your scans. However I found something called a Cine MRI, which sounds far better for detecting adhesions.https://www.ncbi.nlm.nih.gov/pubmed/18322749
I have no idea how available it is, but it is surely worth enquiring into. You could also have exploratory surgery to see if you have adhesions, but the problem with abdominal surgery is, no matter how careful the surgeon is, it tends to create new adhesions - which is the last thing you want.
I don't think your bowel is confused, or at least not that
confused. Post-surgery GI issues usually get better with time, not worse, as beave said. The bowels automatically adjust to their new plumbing; gut nerves regrow and relearn to communicate with each other. It does take a while - anything up to a year - but I don't think there is anything which can hinder that process permanently.
Also, even if active Crohn's can't be found, with your history I would go on a biologic. You never know, it might help with the pain.