Even though antibiotics work for you, they may not be addressing the underlying problem of cuffitis, where there is continued UC in the retained rectal cuff. I am wondering if you have tried mesalamine or hydrocortisone suppositories for this, as they are the usual treatment for cuffitis, not antibiotics. Since you also get oral aphthous ulcers, perhaps oral mesalamine is needed, such as sulfasalazine or Pentasa. Of course, you can also get into Imuran, methotrexate, and/or biologics too.

Something to discuss with your doctor to be sure, unless you want to be on antibiotics full time.

Jan

The only thing that seems to have a positive affect on, what is left of, my GI tract, is the antibiotics. They firm me up significantly and reduce the frequency in which I need to use the bathroom. I sleep through the night when I am on a cycle of antibiotics. I have tried both Canasa Suppositories and Anucort Suppositories, they have minimal effect, unless I am not using them for the correct duration. I take Bentyl and Lomotil 3 times a day, but again, as soon as I stop the antibiotics, the symptoms return. 

I agree with Jan, as I usually do. If you're getting aphthous ulcers in your mouth (and they do hurt like heck!) then oral IBD medication would probably be worth discussing with your doctor. Like CT I'm on antibiotics full time, with good success over a period of years, but that's generally intended for pouchitis that won't stay healed otherwise.