Ellison, a hacker who is working on a 3D printed version of Stubby, emailed me yesterday to share his progress and to inform me that there was a bug in the previously uploaded servo layer of the .stl files - two of the screw mounting holes did not line up with the other layers. He has graciously provided an updated file, and has permitted me to share the pictures he sent.
I have added the updated .stl file to the 3D printer source files (I have kept Joshua Thomson's original design as well; the updated one is called Servo layer - Alternate.stl. Anyone who prints their version should verify which one makes sense for them.)
Ellison's version of the servo layer, along with a photo showing the alignment between it and bottom layers, can be seen below: