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 don't recommend downscaling as it would make everything smaller and break ergonomics.
You can either print these parts vertically, or use your slicing software to split them and later put them back together using superglue or by friction welding.
Let me know if these work for you, otherwise I'll think of something else.