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 double-checked my Fusion 360 files and the holes are 25.4mm.
I even downloaded the .STL files from Thingiverse and imported the meshes into Fusion 360 & compared them and they match perfectly.
What type of pipe are you using? Is there a chance your pipe dimensions are not uniform?