There is a John Shaw article on scanning with Nikon scanners (at the time the 4000 was the state of the art, and is pretty much the same as the 5000). I don't have the reference to the article at the moment but think that you could find it with an internet search. In the article Shaw discusses the basic scanner settings, makes recommendations and discloses the settings he uses and the reasons why. I think it might be helpful to you since you don't have experience with using the hardware or software.
The Nikon scanners, if used properly, do produce excellent results. I had a 4000 and now have a 9000, both of which have performed very well.
Be sure and scan at 4000 ppi, the maximum resolution of the scanner!