How can your get your body's bacteria back to normal?

a few years ago - I had an 'infectious m' in my abdomen - i was on 1,000mg of Cipro a day and another 2,000mg, of Flagyl - for 4 weeks! and after they took the appendix out (like they should have) it was such a mess that i was on Keflex for another 2 weeks. At the end of all that - I was a walking yeast infection - , arm pits...all the warm areas. So then the Doc gave me Diflucan to take one daily for 5 days. Cleared up the yeast but I can't help but wonder if there are still problems - I have tried acidophalus... any other ideas?