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 know what is going on - the OpenSCAD is correct but it does appear the pre-generated/downloadable STL for the 80mm fan version had the wrong dimensions all over. Not sure what why it ended up like that (I have correct versions of the 80mm printed / pictured), but anyway I re-generated that particular STL from the OpenSCAD source and verified it has the correct dimensions now. I also printed a bracket and verified physical dimensions. Let me know if it works now, and if you still have trouble with the screws start with the Customizer and use more relaxed parameters for the screws? Thanks for insisting on this one, otherwise I would have never noticed!