Pulled the canopy and trimmed the sides so the bottom of the canopy is approximately level with the joggle in the canopy frame. No more trimming on the sides, I am right at the level I want for the Sikaflex.
The net effect was lowering the for the forward edge slightly. I still have an issue with the right side at the "ears" where the canopy edge goes from straight along the side to the curve over the top of the fuselage.