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.
Is this what you printed? The notch in the top of the lower portion of the main axle helps alignment. You'll just need to make sure you don't have it 180º off.
If you are looking at the step drum upright with the teeth of the step drum to your left, the flat part of the flanged portion of the lower axle should be facing you. The build manual has a photo of the correct orientation (also on instructables).