MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Did you use PLA? The issues you described sound to me like the printer was overextruding. There are a couple videos of people putting theirs together. One of them is here: https://www.youtube.com/watch?v=5hD_ZGOuvJE
I do know that another user here is working on an actual step by step instruction video and should be available soon.