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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Heh, nah it happens, it's kind of a pain to keep track of everything. I don't know about the distance/dimensions tho, like... I'm a code monkey, I import() an .stl, make lots of squares, then add a million translate() to position things and... voilà !
if I import both designs and line them, your V12 motor mount is ~12.67mm higher, but it's worth double-checking.