As a potentially easier alternative to masking and painting the entire canopy in one shot, you can do a few frames at a time. Cut some good tape (Tamiya Yellow or 3-M blue into narrow strips, and mask off the vertical frames, and paint them. Then mask the horizonal frames and paint them. Maybe there are a few angled frames, particularly on the windscreen portion, that need to be painted, so mask and paint those and you're done.
The process is a bit tedious, but the masking is a lot easier. When using this method, it is a good idea to spray you flat overcoat as you go, because it might slightly change the paint color, which you'll want to match the rest of the aircraft.
As far as fixing mistakes and modifying clear parts, you'd be surprised what youl can do with a fingernail polishing stick and Future floor finish. You can pick up a polishing stick in the beauty supply section of your local drugstore. They have three different surfaces of progressively finer grits.
So if you have a mistake or simply need to alter the canopy in any way, use your normal cutting and shaping methods and finish with sanding with 600 grit wet sanding. Then use the polishing stick, and progress through its three surfaces in order. Finally paint the surface with Future floor finish, and set the canopy aside. After the Future dries, you won't be able to tell that anything was done.