I pretty much only used automatic scan - auto focus, auto exposure with normal ICE. Note that ICE can't be used with true b&w films. I also use exposure level controls to reign in the highlights particularly on slides. Nikonscan color results for me have been near perfect across all the films I have ever used. Occasionally, I would try other scanners just to see how the Coolscan+Nikonscan compares and here are a few examples of completely aberrant results from other scanners that make you wonder if they are even of the same frame of film.
This one using Kodak Gold 100
This one using Kodak Ektar 100
To get the most range out of a film, you might have to post process. I use ACDSee's Light Equalizer on this Kodak Portra 400 to draw out the details from the dark and light areas.
Scanning multiple frames for stitching is so easy with Coolscan+Nikonscan and Kodak ICE. This one of 4 frames of Kodak Ektar 100.
If the film grain bothers you, I would suggest not using Nikonscan's GEM but use grain reduction in post. This one using Fuji Superia 400.
The effects of Nikonscan ICE on detail. This one on Fuji RVP.
You might be really late scanning, but I can assure you that you picked the best possible tool to do it. Of course the Coolscan 9000 is perfect for scanning Kodachrome due to it's implementation of ICE - no abberation even magnified. This one shows DSLR scanning using a Nikon D800 which of course has no ICE compared to the 9000 of a particularly dirty frame of Kodachrome.
But of course the workflow is so much faster with the Coolscan 5000 due to the film handling. Scanning speed per frame is also faster with the 5000.