Hi
There is a good safe bus service BETWEEN CITIES in Rwanda.
It is difficult to get to Nyungwe and impossible to get to see the gorillas without organized transportation.
The alternative to an organized tour is therefore to rent a car and driver. This can easily be done. The usual rate is $250 US per day but you can often bargain down to under $200.
I can recommend Emmy Runiga at the Kigali Tour and Travel Agency, runiga2000@yahoo.fr .He is pleasant reliable and has access to decent vehicles, and will accomodate your itinerary.
Remember there is a US $ fee of $ 500 for a gorilla permit, which you have to get in advance, best by paying for it in cash in Kigali.
There is an excellent Rwanda travel guide from Brandt. Lonely Planet East Africa also has some info. You should read one or the other.
Have a great trip!
John