Caution: I am not a repair technician. This is just what I did on my own D300 body.
First, there are two hex screws inside the mirror box on the left side (right side as you're look face-on at the camera). The one closest to the mounting ring adjusts the focus of the AF-focused image on the viewfinder's screen. It provides the mirror's stop position. The second, and more important screw is behind the main mirror, and adjusts the stop for the AF system mirror. This is the main one you'll want to adjust if you're having a focus issue.
Use a fixed focal length lens. Use a fixed focal length lens. Use a GOOD fixed focal length lens. If you don't have one (which is known to be properly calibrated) go and rent one. I had months of trial-and-error using my reasonably-expensive Sigma 70-200mm f2.8 lens until I realized that it was subject to about a 1.5" focusing error at 6 feet (minimum focusing distance for that lens). Using my 50mm f1.4 was a cinch, and I ended up finally nailing the focus in just a few minutes time with it. Once you have it set at a small, but sharp f-stop (I used f2.0 on my f1.4 lens, it still has very narrow depth of field), check it with all of your lenses (and teleconverters).
The hex screws work on eccentric-shaped pins. Moving the hex wrench up moves the pin back, moving the hex wrench down moves the pin forward. There is a VERY small range of adjustment needed to move the focus point quite a bit. For the front hex head, up on the stop pin moves the focused image closer to your eyeball. Down on the stop pin moves it farther from your eyeball. It is a reflected image off the mirror, after all. Attention: Do not adjust this until AFTER the camera is taking sharp photos, confirmed on your monitor. For the rear hex head, down on the pin moves the focus FARTHER from the camera, while up moves it CLOSER to the camera. In this case you are moving the image forward and back on the focus sensors mounted in the floor of the mirror box. Hopefully your lens is doing its best to resolve the image properly at the sensor plane.
If you find you're taking big swings at it, something is wrong with your lens (as I figured out somewhat late). Any focusing error up close will be grossly magnified when shooting in the distance. If you optimize your AF system witha front-focusing lens, shooting at infinity will be impossible (it will all be blurry).
On the bright side, if you've gotten to the point where you want to try this and you simply cannot send your camera to Nikon for 3 weeks, give this a shot. It's fairly difficult to massively screw up your camera beyond the point it already is, and if you do, there's always Nikon Service to fix it.
BTW-I used both the "Sensor Cleaning Mode" to adjust the screws and occasionally simply lifted the mirror carefully with my finger and used the allen key on it. Be prepared to have to dust off your sensor if you use the "Sensor cleaning mode" as all sorts of dust will land on it while the shutter is open.