I just finished up scanning 1300 of my wedding negatives on a LS4000ed. I bought the Vuescan license, and ended up not using it because of the reason you stated, along with the less than ideal user interface. I went to Nikon UK's website and downloaded the new nikonscan software that comes with the latest scanners (LS5000) and not only did it work with my scanner, but it does a hell of a better job batch scanning.

There are some general tips available at might be a good starting point if you haven't already gone there.