To get a handle on this I took a RAW picture outside in sunlight that included a gray card. Verified in PS that the RGB values were the same (check). Then I opened the file in Nebulosity and debayered with every setting possible (hair shirt? check). Then I wrote down the RGB values reported by Nebulosity for the same spot on the nominally gray card and selected the conversion profile that gave the "most gray" (equal RGB) values (double hair shirt, check).
Next I proceeded to reprocess all the images with the new setting. Which, by the way if you are reading this and happen to be in same situation and don't want to spend 2 hours going through the exercise the answer is ... ta-da ... straight color scaling (not a specific camera like stock 40D or unmodded 300D or whatever).
After all that I cropped and did a Auto Color Balance. Saved every file en route. Then I post processed the image in Nebulosity. The spirit was willing but the body was too weak to start postproc in Photoshop.
The image is still too pale, greenish bluish or something. And I have orange star halos, some noise to bang down and so on. After some well deserved rest I'll tackle the image again in Photoshop to see what I can do about color issues. In some sense I like the more muted colors. Going forward I'll have to think about how I will use colors in these images. But, for now, here is M31 in all it's Ghost Ranch glory.
As for all images ... click to see a larger version.