I just returned from several months of work in South Sudan. I would not recommend you plan a ride through there just yet. There are a number of things that could cause you more grief than you could ever imagine on a trip.
1) The government is in transition right now. Although there is no longer any fighting arising out of the north/south conflict, there is still a great deal of tribal fighting (e.g. over marriages, cows, land, stuff like that) which has been going on since time immemorial, and there is no police force of any kind. This means, if you get into any kind of problem, there is no-one to arbitrate it for you, and there will be no consequences for anyone who decides to kill you.
2) Infrastructure? Forget it. Unless your moto runs on diesel fuel, you probably won't be able to buy fuel for it.
3) What tiny amount of services are available - e.g. lodging, stuff like that - are horribly expensive now due to the influx of NGO's arising out of the recent peace agreement. Plan on over $100 a night to sleep anywhere that might give you a roof over your head and the possibility of washing up in the morning.
4) My experience, gathered from many years of working in conflicts, is that security is usually worse right after the formal end of a conflict. Everyone is nervous, the economy has not yet started back up, and everyone still has their gun.
Give it a pass for the next 2 years, then have a look at it.
PanEuropean
PS: During this past rotation (Nov-Feb), I never even saw a tourist/trekker/overlander in Lokichokio, which is the Northern Kenya gateway into South Sudan.
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