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 am using Simplify3D. It is far more strict about the integrity of STL files. When run thru Model Repair Service, the files get repaired just fine, but most of your files will not print correctly as is. For example, the holes in the electronics shelf get filled in by S3D because it complains about non-manifold edges and self intersecting surfaces.
Also, just to note. I had two NEMA 17 stepper motors to use for this project, same as the ones used in my Prusa I3. They don't fit in the motor shelf because the section in the center that was apparently once there for the IMU, is too wide, so I had to bring the STL file into Sketchup and remove it since the instructions now call for it to be applied with double stick tape to the electronics. Maybe including the dimensions of the steppers you used would be helpful to others who want to make this.
I have most of parts printed now, including a NinjaFlex insert for the wheels. I ordered the electronics kit from the website, but wish it would have included the power switch or was sold separately as I had everything else. I may have to end up modifying the top shelf to adapt to a different power switch.