Originally posted by rawr I know you ask for lenses to be ignored for the moment, but you can't really assess the camera in isolation from them.
Check your favorite lens on sites like photozone, lenstip.com or dxomark, and find the settings (focal length, aperture, vignetting etc) that deliver the best or 'sweet spot' for resolution. Marry that with the in-camera settings you have identified for same.
Plus think about your lighting. You don't mention that as a factor in your resolution project, but it can make all the difference.
Just off the top of my head, not checking it through, would it help to set the set the camera to programme mode with MTF priority? Obviously the dof required for the target changes with different targets, but it might be a good starting point.