One thing is also to accept that AF can be within tolerance, but still not there where you thought it would be. If I remember correctly, AF is good enough if it hits within 1/3 of the DOF for setup used. Meaning that if DOF is 3 cm, for the focal length /aperture used, it's ok if AF hits at 2cm (0 being "beginning" of DOF, 3 being the "end" of DOF area). This would mean that the image just might not be that 100% sharp that you were looking for.
At this point: please correct me if I've understood it wrong!
At least my terminology sucks..
And yes, remember to apply sharpening. AA-filters in your camera makes images looking soft, you need to PP them to get the sharpness.