I have a similar setup. The only thing I'll say is that the rotors seemed to have a longer break in than the standard Avid ones, but I find that to be the case with Shimano rotors in general. Maybe I'm crazy. In any case they work great now.
You may want to consider, however, just getting the Rockworks/Problem solvers/etc 6 bolt adapters. They're not too expensive and will let you use 6 bolt rotors with center lock hubs. When I did my setup I got a deal on the Shimano rotors, otherwise I would have gone that way.
As for long brake cable runs, most LBS should have long cable, and Spools of housing. That said for mechanical discs you may want to look into a housing setup like Avid flak jackets or Nokon housing.