For a West - East trans africa crossing to East Africa there are three main options open to you :
1) Cross sahara West - East and then take a ferry down the Red Sea to East Africa
2) Cross Sahara into Chad and then into Sudan and South to E. Africa
3) Cross Sahara North South and then into DRC (Zaire) to Uganda
The first is the low risk option but it is perhaps a bit of a cheat if you are being a purist. The second two options are quite possible albeit you wont find commercial tour operators doing the trip for insurance reasons.
At the moment there is about to be a coup in Chad but to be honest with you it is unlikely to affect much on the ground.
You can still cross through darfur (its an enormous area and not packed out with gun toting militia as one might suspect) DRC borders are also open and the country is still very undeveloped - which may appeal.
Personally I'd go through Darfur. Route would look something like this: Morocco, Mauritania, Mali, Niger, Chad, Sudan and south. If you had the energy you might also make a foray into Algeria (Tamanghasset) from Mali (Gao) - visit the Assekrem and then head south from Djanet into Niger.
Good luck to you, people may think you are mad but with a good vehicle and a local guide, for the parts that concern you, you'll have fun.
[This message has been edited by ctc (edited 24 March 2006).]
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