From my experiences, here is my two-cents of how to do it.
For exposure, only use Aperture priority mode or Manual mode on the camera. Avoid Shutter priority, Program and other auto modes, as you should keep aperture value consistent across all images. Even with Aperture priority mode, you need to make use of the AE-L (auto-exposure lock) button so that all images will have same exposure, instead of one being brighter, another one being darker. It looks bad if one part of sky is blue, but the next part of it is white. Use smaller aperture f8 or f11 to have large depth of field, to have much of the scene to appear sharp.
Switch to manual focus mode on your lens. If you choose AF-S, single servo auto-focus mode, (AF-A and AF-C are no good for our purpose here,) after making the first attempt of auto focusing — press shutter-release button half-way, still switch it to manual focus on your lens, so that the focus plane won’t change across all images. There is, of course, another way, which involves changing the behavior of the AF-L (auto-focus lock) button and use that button to do the focusing job, hence the shutter-release button won’t try to re-focus for each image.
For focus area mode, switch to single point mode and use the center point to focus, as the center of any lens has the best image quality and best focus accuracy.
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