How's the THX 1138 preservation coming along?
While over at the Song Of The South preservation thread, something came up that I thought you might like to try here. They are using DaVinci Resolve lite (a freeware version of the commercial program, with limited functionality) on their faded 16mm.
http://originaltrilogy.com/forum/topic.cfm/Song-Of-The-South/post/643982/#TopicPost643982
One function in their processing stream is for luminance stabilization. We hadn't tried this but it might be something to consider. (There might be an Avisynth filter/script for this to use if DaVinci Resolve isn't convenient.) It would make a single color correction work better over the length of the movie.