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.
I did this last year when I was having all sorts of issues which turned out to be the Bowden tube connector. Its not bad, I suppose, given the issues I was having at the time.
IIRC, this was done with a fairly standard Cura 0.1mm profile.