Tonight I drilled the first set of holes in the canopy. Everything went well and the holes were as accurate as I could have hoped for.
I made a small sighting tool by bending a piece of aluminum to 90 degrees. I used this to sight a spot on the canopy that was directly over the hole in the underlying frame, then marked the spot with a sharpie. Then I taped it to the side of the hole to help me keep the drill square. Then I lined up the drill on the spot, checked the placement, and drilled the hole.