Pouchitis doesn't generally cause indigestion or heartburn (or substernal pain). One off-the-wall possibility is that you could have Helicobacter pylori (the bacterium associate with peptic ulcers and gastritis). Cipro isn't usually used to treat it, but it can work against H. pylori if the stomach acid is reduced (e.g. with PPIs) at the same time. There is an easy breath test for H. pylori, though sometimes a blood test is done or a tissue sample is taken during endoscopy. Good luck!