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.

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Thats strange - mine is perfectly aligned and i did not notice anything...

As for version without rotation - this was my first version of that rig, and in BLEND-file you could find layer with this version - but i do not advise it since distance between lenses is WAY TO BIG for comfort watching. Moreover - original gopro rig is rotated too - and this is not coincidence ))