HOV,
Don't think "near" the windings. Think "past" the windings. eg if the exhaust vent is AT the windings then the air will flow out of the exhaust instead of over the windings to cool them first. Like with ANY centrifugal fan the exhaust is AT THE PERIMETER. The shape of what we have to start with makes getting it at the perimeter difficult, so we settle for as close to the perimeter as possible for all portions of the holes.
Since you like to analyze things to death, and you have access to a machine that can cut almost any shape holes anywhere on the piece of metal, you should start at the beginning. You have 3 things so far. First, because the covers also support the full weight of the bike we have to leave enough material between both the intake holes and the exhaust holes to support the bike. Second, exhaust needs to be at the extreme perimeter without ruining the lip inside the cover that lock the cover in the magnet retaining ring. Third, the bigger these openings, the larger the debris that could potentially get in.
Another reason the exhaust needs to be at the extreme perimeter is that the magnetic gap is at the perimeter. For air to flow well through the gap, it needs to be able to eaily flow out.
The shape of the holes is also important. The air inside the motor is spinning, and centrifugal force pushes it toward the perimeter. We don't want to disturb the resulting flow, and if possible we want to enhance it, so to optimize the system we have to consider how it moves relative to the outside environment. Think about how the valve stem on your bike tire moves relative to the outside world. When it's at it's closest point to the road, for that instant it is stationary relative to the road and the outside world. As the tire rolls forward, the valve stem accelerates upward and forward in an arc to it's fastest at the point furthest from the road before moving back down and decelerating back to zero. The holes in our covers move the same way.
If I had a machine that could cut anything I wanted, then I would have it cut slots that are shaped in a manner that the remaining material at the perimeter of the cover was shaped like backward curved centrifugal fan blades. Actually, because they are exposed to the outside environment, I would shape each like an air foil in an attempt use the influence of the air in the outside environment to stimulate the natural centrifugal flow by creating a low pressure region behind the trailing edge of each "blade" as it moves through the environment without adding turbulence or causing a scooping effect, which would stuff up the flow. This shape will also help deflect debris and water from going into the motor.
I've actually cut angles slots as exhaust vents in a set of side covers, but it was expensive in the form of using many dremel disks and it was very time consuming, so I never recommend it. The end result looked quite nice though.
You'll find the resulting shape to be angled slots with sharp edges (the leading edge on the inside and trailing edge on the outside). Be careful in the programming, because angle in the cuts for these slots depends on whether the cover is for the left side or right side, and if you get it work flow will suffer drastically, because they will try to scoop air in at the same time centrifugal force is pushing it out.
For the intake, instead of slots parallel to the axle like for the exhaust, I would cut even narrower slots (to keep debris out which can obviously flow in the intake easier than into the exhaust and whatever grit and sand does get in can flow right out of the exhaust). The goal of intake is to allow free flow of air into the motor. That means as much cross sectional area as possible, and to the extent the holes can be shaped like blades that "scoop" air into the motor it is a good shape. Again, the angle is important, because it is opposite on the left and right sides. I would cut many slots running radially from the axle, and stagger the roots of the slots to make room for more of them.
John