I heard last week from friends in Juba that Jet Fuel was in very short supply there, perhaps because the normal logistics and resupply routine has been overlooked a bit in all the excitement surrounding the recent referendum.
For that reason, I don't think that trying to route through South Sudan would be prudent, unless very firm confirmation can be obtained that the required fuel will be both present and reserved for the aircraft being ferried. Keep in mind that the PT6 crowd can use avgas in a pinch, and just might do that if there is no jet fuel around, but the avgas crowd cannot use Jet Fuel.
Michael