Can my chronic abdominal pain, diarrhea, very smelly stools, lots of mucous in my stools, chronic stuffy nose be caused by an imbalance in my gut flora?

Yes. That is one possibility and the easiest to correct. Get on a probiotic ( over the counter) and take it daily and see if that helps.. If symptoms persist beyond two weeks, despite doing thT, then see either a gastroenterologist or colon & rectal specialist. The pharmacist can help with the choice of probiotic.