On my last project, I made separate balsa floor that snugly fit inside the canopy.
Then I cut a hole all the way through the fuselage.  Then I sanded the hole so the canopy-and-floor assembly was a tight fir to the hole.
Then I painted the floor, did that interior detail complete with pilot, and effectively made the cockpit/canopy a finished module.
The module was then glued into the hole with silicone, the gap filleted in with putty, and the finshed product painted.

It's only a Carrier job, not a masterpiece stunter, but the theory's the same.  The cockpit/canopy is firmly locked in, not just surface-glued, and the work was done offboard, not on the whole model.

A way to get a good "seat" on the canopy is to trim as close as you can with scissors. Then temporarily tape or glue sandpaper (180 grit or so) to the surface (fuselage) that the canopy will be mounted upon. Take the rougly cut canopy and slide it back and forth along the sand paper that you previously attached. It will not take long for the bottom to conform to the shape of the mounting surface. Than proceed with the cutting of the groove etc. Be sure to remove the sandpaper before gluing the canopy onto the fuselage...(sorry, just had to throw that one in). 

  Pete & Tom, You guy's ain't right, y'all just ain't right..  LOL