MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I edited my last message with this info, but I'm thinking you might now get the "an edit has been made" notifications, so I'll post a separate reply now:

UPDATE: It looks like the extrusion was right on. I did adjust everything else. But I'm still getting the same issues. I've included a picture of the 2nd print as tight as I can get everything together.

I'm having a hard time setting time aside to learn how to split the file. IF it's not too much trouble could you upload the parts individually? I'd love to get this working.