you may be able to use both scanners
at the same time; ie, the 4000ED scans one strip of film while the 5000ED scans another.
I tried the same thing
unsuccessfully with a Nikon 4000ED and a Microtek 5700. both are FireWire scanners and that's where I think the problem was; I only have one FireWire bus. fortunately for you, the 5000ED uses High Speed USB so your scanners will be using different buses. (scanning film at 4000 dpi via a FireWire 800 bus would have been nice though!)
if there's any chance of getting both scanners to work at the same time, you will almost certainly need two installations of the SF software to be sure that SF is not trying to use the same set of Nikon MAID drivers for both scanners at the same time. see my
posting in the Tips and Tricks section.
you may have one other problem. the newer versions of SF Ai save the preferences in the user's Preferences folder rather than in the SF folder. the question here is whether SF Ai Nikon 4000ED and SF Ai Nikon 5000ED use the same preference set or individual preference sets. you'll know the answer if you look in ~Library/Preferences/Lasersoft Imaging/. for instance, the preference files for my 4000ED have "LS-4000" in their names.
give it a try. it may very well be possible.
regards
Gregory