Probiotics, baby, they'll help repopulate your stomach with the good stuff after all those antibioitcs. But yes, still talk to your doctor for sure, and make sure he likes the probiotics.
Antibiotics do cause diarrhea, so make sure you keep yourself well hydrated, but also address this with your doctor. I'm sure he can recommend something for this. I know there are OTC medications but because of your medication and condition I would talk to him about it. Take care...