Hi Again,
I'm not so sure of my North Sudan directions but if you reach Malakal remember that it is a disputed area between North & South. If you insist to go there I have a mate or two there who might be in a position to offer a cold  .
The quickest way down from there is to cross the Nile (you'll have to find someone to take you across) and come down via Waat, Ayod, Dukpadiet, Panyagor until Bor then Juba (that should take you around 2-3 days). Malakal - Ayod still has active SPLA patrols of 60 + men from time to time, so don't be surpried if you see a lot of military. They will be interested in you.
After Ayod you will travel for a while down the canal that was supposed to divert the Nile, built sometime ago by the Russians but abandoned during the war. There is the wreckage of the (at the time) largest machine in the world that was making the canal, crashed MIG jet fighters and all kinds of game including leopard!
It's very difficult to find your way from Ayod as the road is not much more than a sandy track & you have to know where to turn sometimes at junctions as there are no people (amazing for sub-sahara Africa) and of course no signs.
If you still want to go, make sure you do it before January of next year.
!!!DO NOT ATTEMPT THIS AFTER JANUARY 2011!!!!
There is a referendum at that time which will decide if the South will split from the North. Almost everyone here believes this will lead to a return to fighting.
Good luck mate. Let me know what you decide to do.
CJ.
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