I would not waste my time sending the lenses and camera in to Nikon.
You have been spoiled by comparing your D90 to a D700. I can see by your history where you have been lately. You are being unreasonable. You are hung up on precision.
Let me hep my making some adjustments to your head so you can be happier. Follow samjstern's advice. Leave it alone.
Now, after that I am going to give you another tool and something else to think about. You were using Jeffery's target and using the black characters which are way off axis. That makes you susceptible for parallax and astigmatism errors which really do not effect your primary focus point.
The green dots indicate the point of sharpest focus for horizontal lines. The red dots show the sharpest focus for circular lines. The blue dots show the sharpest focus for almost vertical lines. This is the left side of the target. The right side is identical to this. This is the most popular lens sold with the D70. It is no wonder that there was a hysteria about back focus. This particular lens does not rotate the zoom assembly at different zoom ratios and the focus lens is in the rear, near the camera body. Other Nikon lenses like the 28-200 D rotate the zoom assembly and the focus lens is up front.
The following image was taken at 70mm with the 18-70 kit lens. The busy field focus was used and the focus sensor has been drawn in for reference. There is a decided backfocus with this lens, but the horizontal line focus actually moved closer to the focus point near the edge of the image. This would have looked OK as far as the horizontal line sharpness on the Tim Jackson target but you would not have been able to accept the center image at "FOCUS HERE" on his target. In all fairness my own previously published target would have done the same thing.
This image has a rectangle selected for the circle to the left of the image. The Std Dev indicates 71.54. The top circle may measure 65 indicating less sharpness. Another important thing to notice is the shape of the histogram. There are two distinct spikes, one indicating black values on the left and the other indicating white values on the right. The middle of the histogram indicates the values at the edge of the lines, the values that are not the line or the space between the lines. The distance between the spikes show the contrast of the image. If you use an editor that does not have Standard Deviation, you could look at a selection of a histogram and get a good idea of the focus.
This image shows an out of focus condition. The spike representing black is not there. What is happening here? Remember that we are working with positive images in digital photography. We are literally painting with light. If the image is out of focus the light is being scattered and it therefore goes to the black areas to reduce the blackness. It is light pollution. This is the same target as above but the circle selected is further from the focus line. You no longer have to make a value judgment using your tired eyes. Out of focus now has a number. In this case it is 46.08. Even if you don't have Photoshop, you can interpret this chart with a histogram.
Now, using Standard Deviation on Jeffery's target go back and check again and don't depend on your tired eyes.
Last advice and I am not going to encourage you to insult your fine d90.
Set your lens to f11 and go out and take some fine sharp pictures with that great Texas sunshine. Remember, this year's 50% crop is last year's 100% crop. Don't worry, be happy!
http://leongoodman.tripod.com/d70focuspart5.html
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http://www.leongoodman.com/balance
http://www.leongoodman.com/expose
http://www.leongoodman.com/d70focusnew.html
http://www.pbase.com/photoleon
http://www.leongoodman.com