MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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Hi ipblythe. The OpenScad file is almost completely parametrizable. You just may change the parameter "filament_diameter" to 3 instead of 1.75, although I'm not sure if a 3mm filament will work with a M5 bowden push-fit connector. I once tried drilling one up to 3.2mm ID, so that a 3mm will fit through, but I had to be carefull no to damage the M5 thread.
Please give it a try! I'm looking forward hearing if it'll work or not.