The color looks fine in the in-progress version. I remember being very surprised at how good the deleted bits originally looked, but then again I'm a person never bothered by deteriorated film elements-especially in older material. So the original footage doesn't look that bad to me, especially as it resembles more of the timing of the original Director's Cut.

Speaking of that, you might find it easier to work with the deleted footage and the older versions (Director's, Theatrical, International) for some shots/transtions so that the image blends more seamlessly.

Those dailies and outtakes from Dangerous Days and the featurettes are going to be a nightmare though. Really beat to hell so I don't see how you can really do much with them, especially since people will usually talk right over them in the interviews.