I've not had focus problems with my D4 (or with my D2X's, which were my only other AF cameras.).
When I first got my D4 a few months ago, I obsessively tried out all the single and continuous focusing parameters. I shot hundreds of images, with many different lenses, and then took them home, and played them back on my 55" HDTV. They were each tack sharp.
I shoot NEF + Large JPEG, and use "Focus Priority" as my usual release mode, in both continuous and single AF modes. Perhaps you were set on "Release" or "Release + Focus", and got some soft shots that way?
I go back and forth on the release modes. Focus, Release Priority, Release + Focus....so many ways to get in trouble!
I keep it simple. That's the way my mind works.
(BTW, the Nikkor 70-200 AF is my most-used lens...)