I was going to comment earlier until I saw that last photo of the young man which was obviously out of focus.
I noticed the slight focus difference between the D3 and the D300 and was going to suggest that you try a -5 and -8 and then a +5 and +8 adjustment just to see if the Fo-Call software or LensAlign system might be worth trying. But, after seeing that last photo, I just don't know. Somethings wrong. I've seen your work, and that's not you.