I've flown a couple of trips to Africa for the USAF. Although we were in country longer than what you're going to be, I'll give you what we were told by Uncle Sam.
1. Only drink bottled water -- absolutely no tap. Bottled waters aren't created equally. You need to know which ones are safe. If you don't know, ask your hotel staff, experienced crew members, or call the US embassy (no, I'm not joking). If the cap isn't sealed, don't drink it.
2. No ice in your drinks. See #1.
3. The USAF made us take 2 antibiotics. We first pre-loaded with Doxycycline and took this during the trip. Then, after returning home, we took 500mg of Cypro. Personally, I didn't take the medicine and refused the Cypro. Malaria isn't the only problem however ... there's several diseases that you are at an elevated risk for.
4. Do not eat fresh vegetables. Make sure they are cooked. I suppose you could eat ones that a pealed. However, know that in many cultures, it is acceptable for human waste to be used for fertilizer. So, make sure you wash anything thats fresh (an apple for example).
5. Do wear clothing that gives you protection. In the urban areas I've traveled, during the day you were ok. At night, even in the cities, mosquitos were definitely an issue. I think with proper clothing and good spray, you will be ok. I can't really imagine why you would be spending a lot of time outdoors in the evening ... which isn't smart.
6. Use the buddy system; don't go anywhere alone. Even if you have a buddy, make sure someone else outside your group knows where you are going.
7. Always know how to get to the US embassy and how to dial it using the local phones. Additionally, check the web for any travel alerts for the countries you're going to be transiting.
8. If you travel outside the city, DO NOT TRAVEL AT NIGHT.
I know a lot of this sounds like paranoria, but you have to remember, you are in Africa.
A good site to visit is
Health and Safety Tips for Visitors to Africa - Staying Healthy and Safe in Africa . It addresses all kinds of concerns and has links to all the websites you need.
-Fatty