I had a similar problem with the Curtiss SB2C Helldiver canopy masks when I built it a few months ago. It took some considerable time to "eyeball" the alignment and guess how it would look once painted. In the end I was happy with how it turned out though.
On the rear canopy sections of the TBD, they are really not too visible once stacked up on top of each other. The pilot's windscreen and pilot's canopy are probably the two most visible once the kit is built if you are building it with the canopy open.
In the past I have simply masked off the outside of the clear parts, then painted it with whatever interior color was used. Next I sprayed right over it again with the outside final top colors. The final touch is to paint the edges of the canopy sections that you normally see when it's opened, with the interior or exterior final colors. It's kind of cheating, but it gives you fairly close results. Good enough in most cases... This is exactly what I just did with my AM Avenger and SBD Dauntless builds.
Then when you look at the inside of the canopy, the interior colors are showing. When you see it from the outside, the exterior colors are what you see. It plays a trick on your eyes.
I'm sure that whatever you decide to do will work out just fine Chuck. Thanks for keeping us all updated.
Take care buddy...