First of all, good for you for pursuing your dream! I wouldn't let your IBS stop you for a second! It might provide some challenges...but what Peace Corps stint would be complete without some of those?
I studied abroad in East Africa for four months when I was 21. During that time I was somewhat sick for about one month and then violently ill for about month as well. Prior to traveling in Africa, I was healthy as a horse and my guts were golden.
I lived with a family at first, before heading into some extremely remote areas. Obviously, I had some diarrhea for a while; everyone does! Everyone who travels there, as well as the indigenous people, have diarrhea, so it's nothing to worry about as long as you are keeping yourself hydrated and don't have any other symptoms. It's annoying, but as long as you are simply running for the "choo" (bathroom) and not doubled over in pain or with fever, you're probably okay and simply adjusting to the new environment. The biggest thing to pay attention to is the presence of fever; anything higher than 101 and you want to get checked out.
I got my first parasitic infection - Giardia lamblia and Entamoebae histolytica - within about six weeks of being there. Not the most fun combination. High fever, profuse diarrhea and vomiting, and nasty stomach cramps. I was treated with metronidazole (Flagyl) and was fine within a couple of days. It started cycling, though, as many improperly treated parasitic infections will. You will be fine for a week or two, then get very sick for a few days, then feel better, then get sick. If you find this is happening, you could have an infection that's not being treated correctly, or you could be getting re-infected again and again.
The best thing you can do is to boil all of your water very thoroughly and don't drink a sip of it unless it's been boiled for 20 minutes. That, above all, will be the key to staying healthy. Also, m&m's suggestions of buying peel-able fruits/veggies and washing them in boiled water is important. WASH YOUR HANDS - a lot. Take probiotics, if you can. And cross your fingers. You won't be able to control everything, especially when you are staying with the locals and relying on them for guidance; once in a while you'll be taking risks, but that's part of the experience. Remember that nearly everyone over there has parasites, and they are generally more than a nuisance than anything else.
IF you are in East Africa and ever need quality medical care, Nairobi Hospital is the place to go, no doubt. It is a first-rate medical center! I had to stay there for a week due to a bizarre viral infection and the care I received was phenomenal, much better than care I've received in the U.S.!
Where in Africa are you going? I was in Tanzania and Kenya, and it was the most amazing - and challenging - experience of my life. I have been wanting to go back since the day I left, just over five years ago.