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 think I might try to tweak the guide pegs so that they also lock into the base horizontally for storage. That would help keep the pieces from sliding around while in storage.
The stopper could also act as a sleeve to slide the parts into. That would keep the parts from falling apart when removing them from storage.