Overnight I figured out how to fix the misalignment of the canopy skirt mounting holes. The nice thing about fiberglass is that you can usually fix your mistakes with enough patience and sandng.
I applied a layer of packing tape over the holes on the exterior surface of the skirt:
From the inside, I used a popsicle stick to force a thin epoxy/flox mixture into the holes. After I took this photo, I came back and squeegeed off the excess flox.
Once that was cured, I removed the tape and did the same thing from the exterior side, to fill both sides of each hole. When that was cured, I sanded it all flush. Here's the result – no more holes:
Then I put the skirt back on the plane, and after a great amount of measurement and double-checking I re-drilled the holes. This time it came out straight.
In some places, yesterday's holes were okay, but in others they were substantially off:
Since the alignment of the skirt to the plexiglass and frame was now acceptable, I went ahead and drilled most of the holes that attach the rear skirt to the C-660 side skirts. There are still a couple holes on either side that need to be drilled (where the obvious gap is in this photo) but I wanted to finalize the alignment before I removed the skirt again.
Without removing the skirt from the plane or otherwise disturbing the alignment, I drilled straight through the skirt, canopy, and steel frame with a 1/8" plexiglass drill, enlarging the holes in the skirt and frame to the final size (note copper clecoes in this photo). The holes in the canopy were already at 1/8", and will be enlarged to their final size of 3/16" soon.
Back on the worktable for more surface preparation and pinhole filling: