I've used the 4000 which unfortunately has been in the Nikon repair shop for several months now while they try to find out what's wrong with its FireWire communication in their spare time :-(
the 5000 is faster than the 4000. if you're scanning a lot of slides at 2000/3000/4000dpi resolution, this may be important to you.
the 5000 uses USB High-speed. the 4000 uses FireWire 400.
incidentally, I think you're lucky to be scanning slides. the Nikon scanners (at least the 4000) have big problems discerning the borders of frames in negative film strips. I purchased the film roll adapter (which costs the same as the 50-slide adapter) and it was basically a wasted of money because without accurate frame border discerning capabilities, I was never able to scan a full roll of film automatically. I have since decided that when my scanner comes back, I will pay to get all of my negatives framed and buy the 50-slide adapter instead, perhaps selling my film roll adapter on eBay.
from what I've heard at the Nikon service centre, the quality from both scanners is roughly the same although the 5000 supports a level III hardware/software dust/noise removal technique.
btw, if your slides are Kodachrome, the infrared dust removal technique will not work. it's a known limitation.
for the record, I used SilverFast Ai Studio to scan with the Nikon 4000 ED on an iMac G4 1GHz (which doesn't have USB High-Speed).
and for the record, the talented (seriously) developer folks at SilverFast once told me that they regard the Super Coolscan film scanners as the best in their range.
if you have any specific questions, I'd be happy to answer if I can.
regards,
Gregory