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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I ran into the same problems trying to fit my Udoo dual. I was thinking about reprinting at 102%, but I think the design is flawed. The connector positions may vary from unit to unit, but between the protruding ports on the front and the switches sticking out on the side, it's impossible to angle the board in without damaging something. What it probably needs is the faceplate for the main connectors merged with the lid.
I do really like this designs lid, using the logo for venting (and the screen was a nice touch).