To be absolutely honest with you, I doubt you have a problem. If you're shooting in NEF mode then the resulting images, before being sharpened, do tend to look soft and your example image in those terms doesn't look that much different from what I'd get out of my D1.
There is one thing that it would be worth you checking for, though: the D1 series cameras have had an issue that's come to be known as 'Back Focusing': when taking a picture of, say, a group of people with a wall behind them, a limited number of cameras have been known to focus slightly behind the subjects. This usually occurs with the wide angle zooms - the 17-35mm f/2.8 AF-S being a particular culprit - but is actually caused by the cameras autofocus mechanism being slightly out of calibration: it's something that can easily be fixed by Nikon.
It's easy to test whether your camera has this problem: if you can get better results by focusing manually then there's something wrong.
On the subject of sharpening, if you have Photoshop you might like to try the following trick: convert your NEF to a 16-bit TIFF in Bibble, load that into Photoshop, change the image mode to Lab Color, select the Lightness channel only and sharpen that using Unsharp Mask. This tends to give better results than sharpening in RGB mode.