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.
Fixed parts are ready. See http://www.thingiverse.com/thing:981794 use them instead of the parts uploaded here.
For your motors use Extruder_Rev3 (Rev2 is for common type of motor with fan). This is quick and dirty fix. I will have to remodel the whole extruder body one day, to make it uniform. Other parts are compatible with both types of motors and fans altogether.
Please let me know how it worked.