MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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Most likely a printing problem on your end. I have printed and built the whole thing. Because I had a little runout due to "elephants foot" I had to trim some parts. In fact, I think I had to trim the mainspring part you referenced. This was not a problem with the design, but with my printer settings. You are probably having the same. I have since adjusted z-axis offset to fix the elephant!