Upload & Sell: Off
I had this frustrating problem with my d90 for a while and decided to take a shot at correcting it myself. I used an allen wrench to adjust the alignment of the AF mirror with good results. In my case, however, I found that as the top AF point became properly aligned, the center and bottom points were out of focus. Similarly, as I made adjustments to align the bottom AF point, the center and top points became out of focus. The reason this was happening is because the AF detector on my camera is not perfectly parallel with the lens plane. Unfortunately, it falls within Nikon's accepted limits of error and they refused to acknowledge the discrepancy. So, I ended up fine tuning my camera for the center AF point, which, in the case of the d90, is the only cross type sensor. I locked the AF system and set the menu to single AF point. As far as I can tell, this is the best fix for my camera. Bear in mind that I am very picky and the differences are only noticeable at a very shallow DOF. I have now become an expert at focus, recompose, and shoot .
For more reading, see my thread from a while back:
Also, keep in mind that very small adjustments with the allen wrench (like 20deg) have huge impacts on the AF system, so be patient. Remember to not touch anything, especially the shutter, with the allen wrench as mechanical parts inside the camera are extremely sensitive and fragile.
Also #2, I needed to use a vice and bend (twist, actually) the allen wrench to make the appropriate adjustments because the box you are working in is very small.
I've been using my d90 for months without problems after making the adjustments, so don't be scared, just get in their and make the changes! Good luck!