I assume you are going south from Khartoum. A Friend of mine did this one year ago and the road was not that easy. Have a look at this for detailed information on his page.
I came from Central African Republic in December 2005 to this border. We had to pass the LRA and it was not really fun but we were able to manage it, maybe we had a lot of luck. In 2005 it was strictly advised to avoid Gulu. We drove from Yei to Arua/Uganda and then via Pakwach to Kampala. See this for the facts.
Peter
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