Jon,
I have 2 suggestions for you. The first, if these images are very valuable to you and your family is to have them drum scanned. There are many drum scanning services on the Internet. You’ll pay between $25 to $50 for a 100 mb scan of a 35 mm transparency. Drum scanners have MUCH greater D Max and dynamic range than anything short of a high end Heidleberg flatbed CCD scanner and will produce detail easily in dark images that a Nikon Coolscan simply cannot give you. I operate drum scanners and the hype the manufacturers publish about the so-called dynamic range of CCD scanners is downright fraudulent.
I am not familiar with the operation of the Nikon scanner, but when you mention changing the "analog gain setting" I am not sure that the machine does anything to change the sensitivity of the CCD sensors. I don’t think that can be done, but I’m not sure. It IS possible on a drum scanner to change the sensitivity of the photomultiplier tubes, and that is one of the great advantages of a drum scanner. Drum scanners can dig down into dark shadows that are just impossible for CCD scanners to see.
I believe that the so-called analog gain settings only change the way the Nikon software handles the scanner’s raw image data. So you are just applying the same kind of curve controls in the scanner that are available in Photoshop after you open the image there. Not much advantage doing it in the scanner.
The second suggestion is a method we used to "rescue" a project that was given to us after it was scanned on a Minolta Dimage film scanner (with very similar specs to your Nikon – for all I know, the CCD sensor is the same in both). The customer was convinced that his "5000 dpi" scanner was the equivalent of a drum scanner (because that’s what the industry buzz said).
All the scans lacked detail due to very poor dynamic range in the shadows, but there was no apportunity to rescan. We had to use the files we were given. We tried all kinds of curves adjustments in Photoshop and we were able to improve the shadows a lot with many different combinations. But when we got the shadows lightened enough, we always blew out the highlights. We could never adequately save both, no matter how many combinations of adjustment layers we used.
The method that worked was to create a copy of each image and re-combine the 2 as though we were working with an under-exposure and an over-exposure. The same way that a digital camera can be used to make several images at widely different exposures that are then digitally blended in Photoshop to capture a very wide dynamic range.
The general method is described on this page:
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http://www.luminous-landscape.com/tutorials/digital-blending .shtml>
(Scroll down to the section labeled "The Layer Mask")
Essentially, you paste a darker version of an image into a layer above a lighter version of the same image and follow the instructions on that page to blend the 2 together.
We applied a huge curve to our images, completely blowing out the highlights and lightening the shadows, saved that altered image (different name than the original), then placed the dark version onto a layer mask above the lightened version for digital blending.
I didn’t think the method would work. I reasoned that we were creating no new data and that re-combining the 2 images could achieve nothing that Photoshop couldn’t do with curves and adjustment layers in the first place. But it DID work. It worked MUCH better than anything we could do in Photoshop with a single image.
(Although we improved the images, they weren’t close to the quality that drum scanning would have done)
If the "analog gain" controls of your Nikon scanner actually do allow you to over-expose your images, then you could actually produce 2 different real exposures which you could digitally blend, and probably get very good results.