I don't know if this will help, but here's my experience. I struggled with poor focus/soft images for quite a while when I got my D7000. I tried all of my different lenses, with results all over the map. Finally one day I tried more aggressive sharpening of the NEF's in post and my images immediately looked much better! I came to the conclusion that either the sensor or the AA filter in the D7000 was different from prior bodies, and needs more sharpening in post. Maybe this will work for you, or maybe not, but give it a try and see if it helps you. It did for me.

Rich