This blog has some good posts about the northern Ugandan civil war. This one especially has some interesting points about the conflict and the LRA, such as
".....though it is obvious, let us be clear: military might is a non-starter regarding the LRA. While rooted in a bizarre cult, the LRA is conducting a classic insurgency against an unpopular ruling authority. This crisis can only be addressed by improving overall living conditions throughout northern Uganda - so that even the LRA lieutenants can see that they are pursing a false agenda."
The AllAfrica article at the beginning is a good one for understanding the depth of suffering that has developed because of the civil war. People such as Kony seem so demented but undoubtedly their craziness also carries genius.