It does indeed sound like it will be great with all the fixes. :) Perhaps individual clean frames from an HD broadcast source of the SE might be helpful in replacing some frames that are messed up? Since it's just a frame here and there, any slight differences in color after correction should not be noticeable.

As to the skin tones, it really does help to be watching on a calibrated screen. My HD plasma tv has been ISF calibrated, and it makes Star Wars look great, but even in the Blu-ray V1 the skin tones are rather too reddish, but not too bad. And it was the price of getting the color saturation up a bit higher elsewhere in the scenes.

This new version, of course, will have even more saturation to the scenes now, so you might want to try that script that isolates the skin from all else in a scene and applies a different color correction value to it. Even if there isn't enough color detail in the source to color correct the skin tones accurately, at least it would allow the rest of the scene to be saturated to any high level to bring the background colors back closer to where they should be without affecting the skin tones themselves. Allowing them to be kept restrained and more accurate and not be pulled along with the rest of the scene and made orange, reddish/burnt, etc. A quick test of how it looks might prove interesting. :)