The problem is in the paint program's generated curve. Whether this is an operational bug or a wrong type of curve, I'm stuck with how they've implemented it -- acceptable for any off-the-cuff proof of concept. HISTOGRAM is an easy way to work, with it's few but critical controls, that instantaneously gives picture/graph feedback. It's great for a quick work-up (and gives one the feel of what's being done).
Note that, in this case, the curve should be a steeper on the high end, to allow highlights without overly washing out lesser bright areas. Shifting the mid-tones slightly upwards will also brighten the scene without losing saturation. (I could probably get it closer with some more tweaking, but I'm assuming you're wanting less by-eye and more by-references.)
When working on the THX 1138 "missing scene", I was looking for an Avisynth plugin to do the HISTOGRAM adjustments on the clip. Instead I found a VirtualDub CURVES plugin that could easily approximate the graphs generated from a test screenshot:
http://originaltrilogy.com/forum/topic.cfm/THX-1138-preservations-Italian-Cut-available-see-1st-post/post/589761/#TopicPost589761
With such a plug-in, one can attain pinpoint control over the resultant graph by specifying actual points for the graph. Of course, you will use whatever works best in your workflow.
I'm thinking, as a first step, the capture should be confirmed not to have crushed blacks or blown-out whites in each of the RGB elements (the combined luminance may distort this determination) across the entire film. Run a program/plug-in to produce a full-movie histogram. From that, I would recommend a second-pass capture, adjusted to fill up the full spectrum, without new crushes or blow-outs, of course. Run the program/plug-in again to verify.
Also, I suggest that all work be processed on the individual RGB elements (such as noise reduction, particle removal, etc.) -- you can continue to combine them for review as the project progresses. This way, adjacent elements will receive only the processing they require for fix-up. I demonstrated this approach in a Star Wars thread:
http://originaltrilogy.com/forum/topic.cfm/Star-Wars-OT-1997-Special-Edition-Blu-rays-Info-by-Team-Blu/post/630232/#TopicPost630232
One thing I discovered on the THX 1138 work was, with a faded print, fade is not consistent across any length of film. This means the print should be luminance stabilized, probably best done shot by shot (to RGB elements, of course).
Do you have a list of things to do? The order of doing them may affect the quality of the outcome.