Puggo - Jar Jar's Yoda said:

See, that's the problem. A telecine capture doesn't ever preserve exactly how one would see the film if projected, because of a myriad of factors. The range of colors you get on the video depends on how the film is illuminated (what type of light), how the lens settings respond to the lighting used, the white balance setting on the camera, etc. Cameras don't work the same as our eyes do. And if you find a setting that works on one scene, it generally doesn't work as well for other scenes... sometimes it's way off. So, if you want it to look as close as possible to an actual viewing of the film, you HAVE to tweak it scene by scene in post.

Can you pause the capture and adjust the camera scene by scene? Another idea would be to do multiple captures with different settings and take the best version of each scene before adjusting in post. If any scenes are really bad to start with, do another capture. I am not sure how hard this is to do, so I may be asking too much. :)

Anyway, I agree with Dark Jedi and am only throwing ideas out there that may or may not help. I am very excited about this project!