I few months ago, I helped a neighbor install a Todd's canopy, and then fit the skirt, Oh boy! The canopy looked great, but the skirt did not fit in the rear at all! Todd's canopies are free blown, and has a different shape than the standard canopy, therefore, the skirt will not follow the canopy around the back. I decided to just make the skirt fit the fuselage, and to let it go where it wanted against the canopy.
Later, the canopy was use as the inside mold, and brown packaging tape was placed over it so nothing would stick. Then chopped up glass and West System epoxy was mixed up and stuffed in between the canopy and the skirt. After all cured, the skirt was carefully ground down to the proper thickness over the canopy. In addition, the skirt was nearly cut through along the side near the back so that it could pull up against the canopy when clecoed in place. Then the cut was filled with glass and West System epoxy.
The scribe lines can be used, but cut at least 1/4 of an inch outside the scribed line until the proper fit is assured.
I used both a diegrinder with cutoff wheel and a dremel to cut the canopy glass and the skirt.