Nikon D90 autofocus problem?

I have a problem. I got rid of 2 perfectly good Nikon lenses because I thought the AF was effing up and it turns out its the camera body. This only happens at the long end of the focal lengths. If all the lenses I have have built-in motors then why would my camera body's faulty motor even be used?
I've done all the obvious stuff to try and remedy and to no avail.

Thanks for posting this valuable question. I'm sure there are many, many others who have given up on good lenses for the same reason.

I did a little research and found this do-it-yourself solution. Hope it helps you.
http://leongoodman.tripod.com/d70focuspart3.html

One common problem with the d90 and any dlsr for that matter is the matter of backfocus. Or front focus.
this is when your camera locks onto a point but is actually focusing before or after that point.

just google it and somewhere (i couldnt find it with a quick look), is a test, whereby you print off a paper with grid lines and then you position your camera so that its on an angle of about 45 to the paper. Then you lock onto one of the numbered lines. For example, the sheet may have a series of line numbered 1 to 20. If you lock onto line number 10, and you see that line 9 or 11 is in focus and line 10 is not, then you know your have either a back or front focus issue.unfortunately you have to take your camera to the shop to have it adjusted.
also note that many zoom lenses do not focus well at either end. For example, i have an 18-200mm nikon lens. It is quite soft at 18-20mm and 180-200. This is common for zoom lenses and not a camera issue.