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Don't be afraid to try public transportation or to bargain. It can be frustrating but a lot of fun!
Travel: I admittedly had the most horrendous luck with travel in Africa, but with numerous delayed and cancelled flights, I did learn a thing or two I can share with you:
1. The SOS insurance is only for medical/security evacuation, it does not cover travel disruptions, so consider purchasing additional insurance to cover that.
2. Kenya Airways averages 2-3 hours delay on its flights, so if you are transferring within Africa, consider a minimum 6 hour stopover. Precision Air was not much better. An extra hour or two in Nairobi airport is better than an extra night and the stress of trying to rebook your flight. Also consider booking one flight earlier just in case your flight is cancelled and you need to hop on the next one.
3. Don't fly Air Malawi. Last year they were booking tickets and cancelling flights for months.
4. I do recommend you book through the MIT travel agent or another agent with an emergency assistance line. They are generally pretty bad at booking flights and they won't work to give you the optimal schedule, so definitely take the time to do a ton of research on your own. However, their emergency assistance line is AWESOME, as long as you can figure out how to make a collect call from Africa (I called home at 1 am in the morning). I had two flights cancelled on my way home (one from Zanzibar, one from Heathrow) and both times they were able to rebook me onto the next flight. There's absolutely no way I would have gotten home without it, and it saved me literally hours of standing in lines (more time to hit the duty free).
5. If you have travel issues at Nairobi airport (this probably goes for most airports in Africa), don't wait inside security - get a transfer visa and go out to the main desks to sort it out. Phone calls to airlines in Africa are also generally useless, just go to the airport to sort it out. Also, you don't need to fly Kenya Airways to use their economy lounge in Nairobi, and they have couches you can lie down on.
6. Pack all your valuables, prescriptions (malaria meds!), address book/phone numbers, and a change of clothes in your carry on including phone/camera chargers (someone had his chargers stolen from his bag).
7. There is a big, squooshy playground in B concourse of Terminal 5 in Heathrow. It's a good way to pass the time if you're bored.