MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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yeah i had similar issues with alignment, i didnt end up uploading my design because i thought dual parallel rails was a design issue, maybe i just had some crap quality rails?
basically my issue was the y axis parallel rails would bind as they were not perfectly parallel, so i basically made one of the rails float to make it workable. you can see the photo of the rig in my titan adapter. https://www.thingiverse.com/thing:1881918
i like your design, i might covert over.