M'kay, to keep these from turning into marathon responses I think we should deal with one front at a time. That being said, I'ma start from the top, and we'll move on to the next one(In your post up there) when we've figured out this one. 

"All that we need to do on that particular front is decide a little bit more how the Organization came about. It isn't something that would have sprung up by chance, since it would take a lot of effort on both sides to set up something that wouldn't fail within the first year or two. So we will just need to flesh out those details."

I see this as kinda simple. Some of the more powerful fighters from both sides that have grown a faint respect for their equals on the other side of the line saw more and more innocents dying now that it is against the peace treaty for the warriors to attack one another, so they came up with the idea with one another, and together they brought it to the leaders/council/beings that drew up the peace treaty, on both sides and when the idea was approved the top warriors were given the duty to keep both sides in line. However, to make sure there was no ganging up on one side or the other, they came up with the two being teams, one from each side, so they could keep one another in check. So in short, all those in power put their backing behind it, and those chosen to work on keeping the peace within the organization were given licence outside the law to keep the peace as they saw fit.

Does that sound good?