It looks like you're using Gamma 1.0 for your SF HDR gamma. That will make a very dark scan. You're also not embedding your profile from SF, at least that what it looks like according to your preferences.
You really want to scan in RGB and preferably 16 bit per channel RGB. If you can set accurate highlight and shadow points in SilverFast, that will go a long way to getting the right, or at least much closer, color. I would set an output gamma of 2.2 and use Adobe RGB as your output profile. When you open your scan in Photoshop, set the dropdown window on the lower left corner of the file to read Document Profile. It's a nice reminder to see what color space your file is in.
From there, you need to go through the standard color/tonal correction steps you'd use for any image - set highlight and shadow points using Curves adjustment layers. Finding and setting a neutral highlight and shadow will take care of about ninety percent of your color problems. If you still have issues like magenta skies, you might need to use Hue/Saturation or Selective Color to address those. You might want a touch of highlight/shadow to control contrast. You might need a bit of sharpening, preferably selectively. Every image is unique.
You want to have your RGB file looking fantastic on your hardware calibrated screen before your even thing about CMYK. After you do that and convert to CMYK, then check your black and white points again for proper ink values. Y'know - a white with a bit of detail at something like 4c, 2m, 2y, 0k and a white with tone but no detail at 1c,1m,1y. From there, especially for magazines, you might check saturated colors for contamination and use Selective Color to make final tweaks to colors and even to the blacks as well.
What scanner are you using? Flat bed or drum? The only thing that will deliver decent shadow detail is a 4.0 d-max ( few scanners can achieve that ). Has your scanner been calibrated? If so, you'd use the scanner profile when scanning similar media ( slides ). In Photoshop, try a Rendering Intent = Perceptual. It's pointless to show us pictures of your files because we cannot see the original(s). There are a few things you can do to bring out the color you are looking for. I'd recommend you get a copy of "Photoshop LAB Color" and "Professional Photoshop Photoshop" by Dan Margulis. Also, what do you have in place for proofing? You refer to screen views, but are you seeing casts in your proofs?
You are trying to do something that is very, very hard to do. Getting a high quality scan of your slides requires that you get not just the color, but also the dynamic range, contrast and saturation correct. The issue with the cloud is a contrast problem, and there appears to be a color problem as well. Here's what I suggest:
- Project the slide on the wall, and adjust the same image on your computer while observing the image on the wall.
- Turn off HDR, it's not for this. Play with shadow / highlights instead.
- Use sRBG across the board.
- Set your scanner for "Perceptual Intent"
- The "Optic film" color profile should be "Default"
When you look at the image on the wall, your eyes take a 500MB image with a million to one dynamic range. The monitor on your computer can only display a dynamic range of 64,000 to 1, and the scanned image is only about 3MB, so you're not going to get it to look as crisp as what you see on the wall. But, there are tricks to get it close! Play with the sharpness and contrast. Your eyes are 50 times more sensitive to contrast than color, so just get color close, and spend your time on contrast.
I took your first screen shot image and saved it as "MountainTop1.tiff", ince it did not have an embedded profile, I applied Adobe.RGB to it. I then saved a copy and named that "MountainTop2.tiff". In the copy I converted the image to LAB. The following screen shots show the curve adjustments and theri results in the copied image, which set next to the original is drastically different. I have no image to compare it to and the screens just show what is possible...
My next step would be to save a copy of the LAB image to RGB via Adobe RGB profile and then save a copy of that image as CMYK using the SWOP web coated v2 profile. Only I have no idea what the original slide looks like projected, therefore the above screens only show what is possible. The above are all 8-bit RGB images.