For that cockpit, I would have masked with small pieces of kubuki (or Tamiya) tape, either made up from small pieces or with each piece cut to size. I also usually dip the whole canopy into Future or Pledge before mounting it, let dry, then I glue the canopy into place with tiny drops of CA glue, or watch cement, or even white glue, depending upon which one I think will work best for each case. Then, add the rest of the glue along the canopy edge until the whole thing is completely sealed, fairing it in as best possible.
One of the reasons for dipping the canopy into Pledge, etc. is that if "smutz' like you have occures on the inside, I can just drill a small hole (usually through the top of nose gear well from underneath, and inject a little Windex with AMMONIA (the ammonia being key here), which will then dissolve the interior layer of the Pledge ans allow me to slush the Windex around the inside of the cockpit, flushing out the crud, and allowing it to settle into an inconspicuous spot down around the seat. If the Windex take too long to dry out, shoot a little drug store alcohol into the cockpit, which will dry it out quicker. The disclaimer is -- do this with enamels; I'm not sure what would happen with acrylics, etc...
Then, I would use Parafilm "M" and mask the entire canopy, leaving just the attaching edge (no more than 1 - 1.5mm clear. Then I'd fill with Perfect Plastic Putty, if it was a good join line. The PPP will smooth out with a wet Q-tip, and you might get away with no sanding at all!
If the edge needs REAL filling, I'd use Bondo Spot Putty and Sealer, and sand lightly with a fine rat-tail file or 600 - 800 grit paper, sanding wet. A light coat of primer here if needed JUST AROUND THE EDGE!
Then, I would unmask the entire canopy, and add the necessary masks. I would do the canopy area first, and only spray the interior color first, followed by the outside color(s). After that, I would re-mask the whole canopy with Parafilm "M", along the lower edge of the glass parts, and spray the rest of the model as needed.
View attachment 582371
You see this technique on my
XP-58 Chain Lightning Build
along with step-by-step photos. Last word of advice -- while all this may seem like a lot or work, it's eventually worth the effort to learn how. All it takes is practice!
Good luck,
Ed