If the “higher up” inflammation is immediately before the J-pouch then I think it’s more likely to be backwash ileitis than Crohn’s. There’s no valve preventing pouch contents from backing up into the neoterminal ileum, and this can cause some inflammation. If the higher up inflammation is elsewhere in the intestine then Crohn’s becomes much more likely.
You may simply be developing antibiotic-dependent chronic pouchitis, and might require continuous antibiotics now or in the future. If so, it’s best to find several different antibiotics that work for you and rotate between them periodically (perhaps every 10 days or so). I wasn’t able to find multiple antibiotics that worked in my case, but Cipro (and later Cipro + Flagyl) have worked great for me for about 11 years.
Some people have had success with very low carbohydrate diets. You might consider giving that a try, if you can stand it. It includes *all* carbohydrates, though, not just some imaginary list of “bad” ones.