Unless you need some new fimware in the scanner because of the new software version I don't see what should go wrong.
I installed a Minolta scanner this week and was obsessive about following the sequence instructions exactly because a lot of people had problems with this scanner and the USB bus, etc. Mine worked properly from the get-go.
In the case of the Minolta what you have to do is install the bundled software package first, the machine then reboots, then you plug the scanner in and fire it up, Windows sees the new hardware and installs the drivers, then you launch the Minolta software and it initializes the scanner. Of course your Nikon sequence may vary, but the point is to follow the instructions in the manual.
When you say you uninstalled everything, use Explorer and examine your Program Files directory to see if there are any files or folders that the uninstall software missed. Then follow your manual's instructions with respect to configuration/install carefully. You generally only install software once so you may have missed something...