I am having a focus problem with my D3 as well. After living in Hawaii for some years, I have some mold growth in my lenses and thought that was the reason for the lack of sharpness. But I see around that D3 owners regularly note a drop off in sharpness over time. I'm about to send my gear in for repair, though the last time I did it cost close to $2000 for camera and several lenses. Outrageous!
That was the Nikon shop in CA. Anybody know of a less expensive shop?
By the way, what is a "D3 re-tune" that I see mentioned in the previous post by SteveK?