In preparation for filling the gaps between the skirt and fuselage, the fuselage under the canopy was covered with packaging tape to protect it from the flox (a thick mixture of epoxy and milled glass fibers) to be applied later. The tape was coated with PVA to ease the release after the flox cures.
I decided to trim the latch side of the canopy skirt to just above the skin rivet line. This will raise the skirt lower edge to clear the fuselage joining fasteners, simplifying the intersection of the skirt to the fuselage in this area. While the canopy was still on the fuselage, and latched in place, this cut line was marked.
The first layer of Bondo was applied to the previously identified low spots on the skirt, and allowed to cure several hours. The Bondo was then sanded, significantly improving the surface of the skirt. At least one more pass with Glazing and Spot Putty will be required before painting the exterior.