MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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The end of nozzle it supposed to be 8.5 mm from the flat of the bodyhttps://www.antclabs.com/bltouch
think you missed half the dimension it is 5.5mm + 3mm
so looks like about 3 mm off or so, very little nozzle clearance.
Please fix if you have time. I will reprint and test it.