A good map and plenty of time
The starting point of a trans-Africa trip is to get "Africa on a Shoestring" and the 3 Michelin maps (links at http://photobiker.com/store/books.html#maps
The Lonely Planet guide gives all the info about the visas. Pay particularly attention to the countries that only deliver visas at the embassy in your home country, meaning that you can't get one on the road. The price for a visa is very variable, anywhere between free and US$50. Bribes are only exceptionally asked. More common are the fake fees at the borders ("With receipt!", they say, waving a receipt book bought at a local grocery store). Only pay fees that come with a government form and always ask for a stamped receipt. Sometimes officials want to see the receipt that comes with the form or the visa.
The Michelin maps are the best for Africa. They show everything from the state of the roads to the availability of fuel, and they usually are accurate. Read carefully the information they give about the rain seasons: some roads are impassable for weeks or even months.
Read everything that was posted here on Horizons Unlimited in the past several years about the few sensitive parts of your trip, especially the unpaved roads and those that you absolutely must take because there is no alternative. Keep a reserve of money in case an area closes down and you need to fly or ship the bike. Learn french if you don't speak it yet (Western Africa is a delight for french speakers).
Finally, I think that 4 months is the strict minimum you should plan for. Personally I would not consider doing it in less than 6 months. Travelers in Africa tend to slow down the further they go, and it's not just because of the sand and the mud. Spend a month in Morocco and the Sahara, another in Senegal and Mali, a few weeks between Togo, Burkina and all the way to Cameroon - and hop! you are already 3 months into your trip and not even half way there. So take your time, you will not regret it. Time is the one resource that's plentiful in Africa. Spend yours with the locals and you will probably be given much more than you came with. It must be one of the reasons why Africa is so unforgettable.
Enjoy the ride,
Pierre (& Merritt too)