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.
My design is based on my delta printer with a bed of 200mm diameter (180mm usable) and 310mm of Z (280usable).
My advice is do not scale the parts since they have inner structure that can lead to wrong results.
You can try to use for example Slic3r to cut the bigger (Z) pieces in sub parts and save to new stl. Of course there is a bit of work in reassembling after printing.