A while back there was a thread on auto-focus fine tuning. I wrote in response to be careful because from personal experience one can make a perfect lens/camera combination not focus correctly. Since responding to that thread (after receiving my camera back from Nikon Repair Service) that the lens/camera combination was not focusing correctly. In repairing my camera the Nikon service tech re-aligned the mirror. I believe that is what changed how the camera and lens worked together. That being said I tried various ways to correct the focusing problem without success until I discovered the method in the thread I will post below. The instructions in the thread explains it better than I can. If you are having problems with the camera/lens combo focusing you might consider giving it a try.
http://www.dpreview.com/forums/thread/3377109