It's also worth checking your camera/lens combo for Front/Back focusing issues.
How do you check for this?
Here's a sample focus test. This one's not really the best, because the focus target in the center (the wider black bar) is not parallel to the sensor, so there's some front/back error possible just in how the autofocus interprets the object. A better target is a separate object, set up parallel to the sensor. You get the idea, however. The paper was set up at roughly 45 degrees.
I think it's also a good idea, not followed in this example, to set up your focus test at about the distance you normally use the lens, since it's possible for the lens to have front focus at one distance, and not at another.
Some Nikon DSLR's have a fine-tune focus adjustment, so you can take a series of shots like this one, and tweak your lens/camera combo.
I hope the image comes thru,
Jim