I agree with Nanners...antibiotics can mess up the digestive system...and stress - good lord - what ailment CAN'T be traced back to STRESS?!
From my experience, if your bowels are waking you up at night, you're in a flare. That's certainly not the only predictor but definitely one of them. As my GI says, "Your bowels are supposed to sleep when you sleep. If they wake you up, something's wrong." When I'm in a really bad flare, I'll wake every hour during the night.
I'm curious as to what maintenance drug you're taking. You only mentioned spirituality, positive thinking, meditation, relaxation, probiotics, rest, eating good, etc. as your healing tools.
Probably. I'm scared to touch medications now and foods, but I'm learning to get through the anxiety of it all. Yes, a bland diet.