If you are still struggling to get sharp images with your 50mm prime lens, it could be that you are not using the sweet spot of this lens. I now shoot exclusively at Aperture Priority mode with this lens and I now find the sweet spot to be at F/2.8.
As mentioned, the Nikon D90 autofocus engine may, at times, be confused on where you want tack sharpness, so give it break by telling her precisely what autofocus mode you desire. I prefer single point on the Nikon D90.
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