Windmill sweeps may appear to go around anti-clockwise from one point of view (the "front"), but from elsewhere, particularly inside the mill, they are going clockwise.
Just speculating, but if the sweeps go clockwise (viewed from within the mill), the brake wheel is of course going CW so the wallower will be going ACW (viewed from above). Therefore the great spur wheel will be doing ACW, and so the stone nuts will be going CW. There is usually a preference for the stones to rotate CW, if they went widdershins the flour would be of bad quality! More prosaically, the stones were "bought in" and I'm guessing would always be cut for CW milling. All suposition of course!
Apologies for not seeing this earlier, but no one normally posts on the mills bit!
Supposedly in modern times, wind turbines turn clockwise these days, due to the efficiency and the earth's gravitational pull, but yes, most mills were built anti-clockwise, and I'm not aware of any mills in Kent ever being clockwise. In East Anglia and the Midlands there are/were quite a few clockwise mills built, and a handful in Sussex.
As for gearing turning in the opposite direction, it doesn't make any difference to ground flour quality, but as Martin R states, millstones were often supplied pre-dressed anti-clockwise, so it became a convention, especially with journeymen millstone dressers who were used to dressing/cutting the stones that way when they needed re-dressing. As an aside, the phrase 'show me your hands' is alleged to relate to millstone dressers and their experience, as the darker the hands (through flecks of stone) the more experienced the dresser.
For me the most interesting point is that areas were full of journeymen millers, and you'd know which way the sails were coming from if you walked out the door!