Hey Ramzey, I found a trick for those Alpha-channel markings...
One of the "blue" planes that I exported from the Terrain Editor (don't remember which now) had 2 extra files, in addition to the normal skins; these 2 files were called MARKING.bmp and MARKING_a.bmp. The first file is a skin of a couple styles of blue & white stars, a Russian star, and a Canadian oak leaf. The second file is the alpha for the first, which clips the silhouette of the markings.
Check your Savedtex folder to see if you have these files already. If not, export a bunch of Blue planes and they will show up.
All you have to do is open the Alpha file, and black out the hole for the unwanted marking. When you compile the shape, the old marking becomes invisible. That's how I did the SBD and TBM.
Only drawback is... any planes that are used in this terrain AND use that markings file will have to have their markings painted directly onto the skins. Not a big problem though.
As for the mystery panels on the B-17...? I think having a 95% green B-17 is still better than not having one. I'm planning to work on this plane regardless of Midway, so if I find any solutions, I'll pass them on.