In the THX 1138 thread, I eye-balled the best middle-ground setting for a "missing scene" (with noticeable fade fluctuation). However, that single setting, used for the entire capture, produced a good result:
http://originaltrilogy.com/forum/topic.cfm/THX-1138-preservations-Italian-Cut-available-see-1st-post/post/589864/#TopicPost589864
and that (color correction) was good enough for the project. So a single setting could get things going.
Regarding reference material, care should be taken to use only that which can survive from the actual work. Packaged production cels are probably it, and the cels alone (not the backgrounds, which are later added for the sale). If dye based original prints are available, that would be a 2nd source. Beyond that, I don't know if anything is trustworthy. Many parts throughout the movie use similar locales -- light areas, dark areas, indoors, outdoors, toondoors. A variety of different-scenes references is key. Whatever is not available, a good guess then could be made from previous settings.
My suggested list of things to do (and probably to be done in the order shown) after reviewing the previously posted sample clips:
? capture
? de-spot (random debris)
? de-scratch (continuous debris)
? de-noise (grain)
? shot luminance stabilize
? frame motion stabilize
? sharpen (non-haloing)
? color correction
? mask/resize/frame (HD, DVD)
(Of course, working on RGB elements is my assumed best-way-to-work.) I don't necessarily know how well this can be done with what's out there. Depending what is used, these steps may be shuffled around. Avisynth has allot of filters and I've seen some that claim to do all of these. Here is their definitive list:
Avisynth Wiki - Internal filters
http://avisynth.org/mediawiki/Internal_filters
Avisynth Wiki - External filters
http://avisynth.org/mediawiki/External_filters
If you're using other software, see if it covers these steps.
For example, from the short clips, I tried a de-spotting filter called Spot Remover. I tested it with it's author's recommended settings but it's cryptic and I have no clue what's going on. Anyway, when it works, it works well:
Problem is, it doesn't work this well all the time (it's a toss of a coin). Maybe the every-fourth-frame-duplication is tricking it.
Also, I forgot to mention more about the VirtualDub plug-in, which was used for the THX 1138 color correction. Gradation Curves (v.1.46b) by BBugBunny, A.K.A. Alexander Nagiller, is easy to use, has interactive adjustment just like in a paint program, but is more flexible. It's good:
:)