Sorry, I Googled for "canon canoscan 9000f mark ii manual" and didn't specifically notice that the manual I cited was only for the Mk 1.
And no, I haven't read all 334 pages - but I did notice that it looked basically similar to what came with my cheap and cheerful (£35) all-in-one printer/scanner a couple of years ago. Looks like a retrograde step if the "new improved" model is not so good as its predecessor.
"However", although it doesn't come with MP Navigator Ex (coming with Scan Utility and My Image Garden - whatever that is - instead) it *does* appear to come with ScanGear (according to
So it might be worth finding that and firing it up and - if necessary - referring to the appropriate part of the Mk 1 manual, because it will probably be very similar).
Incidentally, when you say that there's very little documentation, are you referring to hard copy printed stuff? You'll almost certainly find that most of the documentation will be in the form of an on-screen manual which will have been installed when you installed the driver, etc.