I spend all of march 2008 traveling from Kenya, lockichogio into south sudan and then to Kharthoum. here's a bit of the things i learned
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route: loki, Juba, BOR, Waat, malakal, west around Nuba mountains, el obeid, kharthoum.
The border there is open and it's quite doable to get the permit for south sudan in Nairoby. However the visa for northern sudan will not be stamped here, which is going to be the big problem when crossing in to north sudan.
We found no way to stamp it in the south so just moved on (were told to stamp uppon crossing in to the north as well) but did not happen.
I see no legal way to cros south to north.
Probably crossing in to the south from north will be less problematic IF the northern road block's allow you to proceed down, they probably wont! But... pm me for a road without roadblock (and apperrently no mines, at least i did not find them), the next problem... mines.
The route described by UN road trans guy's is not mined and or cleared though. but that one is blocked by a LOT of checkpoint's.
If you decide to do just the south i believen you'l be OK, just prepare for a hard time with the SPLA/M and very paranoid people on the way. Your basically still traveling war zone in some places.
Border to Kenya is open, border with uganda and CAR is open and even DRC i think is open, basically your free to do what you want there, so be smart in what you WANT to do.
Traveling there, the best thing to do is know the local SPLM leader (commissioner) There are sat phone's around and a call will be made, so dont make your story up, talk to the guy, you will find them very helpfull and usually fun as well. giving the local SPLArmy a name and business card of the county commissioner will help you A LOT!
Feel free to pm/mail post questions on my route if you go in!
I had a great time there, but is was real hard and tricky at some point's. i'm afraid i crossed quite an arrea of mined and uncleared zone becouse of circumstanced.