The focus for a scenic landscape should be set about one third in to the vertical axis, particularly over water where soft focusing will achieve more consistent stitching because of the constant movement and rippling.
In order to attain perfect continuity set both the exposure metering and the focus to manual. Take an exposure reading and keep this the same for all the frames. Allowing the camera to do it's own metering or auto-focus will result in discrepancies. As with any composition you should decide where the focus will lead the eye in the final picture. Set auto-focus to this point and once done switch straight back to manual before you take the first shot.
Keep this focus throughout. Using focus intelligently can create some interesting effects. Although we often think of a panorama in relation to landscape photography, panoramas can be used anywhere you want to increase the field of view, so setting the focus centrally on the vertical plane for example, can create a pseudo tilt-shift effect or a sense of movement as though the viewer is being pulled into the centre of the picture.
Similarly, white balance set to manual.
A special mention must be made here of stars and the moon. If you want to have deep, starry night skies, try to photograph somewhere with a low level of light pollution. Keep the exposure time as low as you can manage because stars move very quickly across the frame. An exposure of 10 seconds or so will begin to trail. Because the position of the stars will change in relation to the landscape below you need to be as quick as possible. Similarly make sure that the moon does not appear in one of the overlapping thirds because it too will move relative to the landscape.
NB Generally I shoot in high quality JPEG but software such as PTGui now offer RAW support and functionality across the range of image formats is improving all the time. If your images are RAW then covert them to TIFF before stitching to eradicate JPEG compression artefacts. Also, don't sharpen or compress the images prior to stitching. This would better be left to perform on the final image.