If you want to test your camera for proper focusing, use the method Thom Hogan describes in this article about the D800. While he wrote it specifically about that D800's left focus error issue, it is a very good description of how to properly test a phase-detect system for AF accuracy. http://www.bythom.com/D800autofocus.htm
If your camera tests out such that there is a difference between the phase detect and contrast detect (live view) AF, then you either need to try using AF fine tune to get rid of the difference, and the same test setup will allow you to easily dial in the right value. If all of your lenses test out to have a very large offset (say +/-15) that is consistent, then the camera body likely the source of the issues.
Also, on these high-end Nikons with many AF sensors, you have to be careful about the AF settings you are using. There are a number of subtle settings that control the AF array, and they can make a critical difference, especially if you are using continuous AF. I recommend reading up on the current Nikon AF systems, either on a Nikon-related forum like FredMiranda or NikonCafe, or the advice of someone like Thom Hogan.
If it is not a camera/lens calibration issue, or a camera settings issue, then you might have to start considering the monkey behind the viewfinder.