Rebecca, also I am not sure if you read the FTD: IBS book, but moderate caffeine and alcohol are allowed. I tollerate coffee just fine, although I suspect I have some lingering candida overgrowth from taking antibiotics for dental work so I avoid alchohol for now and sugar.
Did you ask your holistic doctor about addressing candida? If you took Flagyl you likely have some fungal candida. Addressing this with a safe candida supplement like SF722 can be helpful.Do a Search on Dr. JEffrey McCombs he has some good information on candida. Candida often goes hand in hand with SIBO.
Also, mind/body connection is importat with impaired digestion. Daily medidation could be helpful or other stress reduction strategies.