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That gets me to the third drill bit I modified.  In the first picture, the bit on the right is the #40 I used to drill through the plexiglass. It had the modifications I spoke of earlier.  The bit on the left only had the flutes polished smooth, not the corners.

When I drilled the bows with the first bit it was able to make a nice starting hole in the aluminum but would then bog down and – unsurprisingly – not cut the aluminum very well. I had suspected this so I made the second drill for cutting through the aluminum bows with the canopy still in place.

With the face of the drill in the aluminum and the flutes polished, I was not worried about the bit catching the edge of the plexi hole. This might have been overkill, but it worked very well.  I did not have to remove the plexiglass to drill the bows or drill the bows first and then try and match drill the plexiglass. This is also how I did the square tube on the port side.  The square tube on the right side was match drilled to the hinge before canopy installation.

The third picture shows a pretty fair line one from the windscreen to the canopy.  My windscreen bow is right to the plan, I did not try and raise it.