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.
Thanks for your feedback larry_h. Our suggestion would be for you to slightly modify the length of the arm and the filament spindle so that it fits your needs.
These changes are very easy to make since they are only straight cuts or elongations in one axis. For instance you could use the software netfabb Basic to cut the spindle's filament axel at any hight, move it up and then join the two parts together. Then you would have a long filament spindle. Make sure not to make it taller than what your 3D printer can make.
We will make this modification for you and post a new taller spindle STL file.