Interesting dilemna with the B-17 kit. I'm building the visible version of this kit, so I only have to paint one half. But, the dilemna is; do I paint only the one half and leave the seam line or do I paint the one half and then a bit over on to the clear side (making it look like a cutaway) and clean up the seam?
But on the solid half, I'm painting first, then installing the windows. Too much hassle to mask, paint and then do any clean-up.
What you can do, is leave the windows out, paint each half to within a half inch of the seam, install the windows, join the halves, clean the seam and then finish painting. You'll only have to mask the top turret, the radioman's glass and the canopy glass. You won't have to mask the cheek glass, the waist gunners, the forward observation dome or the nose. Leave the dome and nose off until the painting is done. You could even leave the cheek glass out until then because they are accessible through the front, with the nose off.
-Fred