MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
behn66 made some reducers to allow spools with smaller hubs to be used with the existing cap and nut. Did you take a look at those?
If those do not work for you, I am sure I can come up with something that will.