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.
It's designed to be thin enough to clear the X axis stepper motor. Unfortunately the extruder stepper is in the way on the other side (the arm needs to be at least this length to reach below the hotend).
One thing I have noticed whilst trying to calibrate this is that there is quite a bit of slop in the shaft of the steppers I have. I guess the addition of the bearings at the top of the Z axis threaded rods helps with this at the risk of adding artefacts in the print if the rods aren't perfectly straight.