Puffer, this sounds like pouchitis to me. If you've only had the one course of Cipro then it may simply not have been treated adequately. Sometimes several antibiotic courses, or a higher dose, or a different antibiotic is required. Sometimes antioibiotics have to simply be continued, preferably rotating among several that work for you. The chest infection is probably unrelated to the Cipro, though we can't be sure. Cipro does occasionally cause pneumonitis, which is lung inflammation *without* infection, and if that's what you had Cipro might be off the table for you.
There's no need for you to live like this. I'm on antibiotics all the time ("antibiotic-dependent pouchitis" means the symptoms return shortly after stopping antibiotics). That's not perfect, of course, but I feel great, teach martial arts, scuba dive, and work full-time. You might not need antibiotics all the time, but you do need to get your pouchitis under good control. Good luck!