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.
Everything is already in the proper orientation, at least in my opinion. You'll DEFINITELY want to print those vertical, because you need maximum strength for the trigger pivot, as well as the gear pivot, so those need to be printed in layers parallel to the bed, and not concentric circles. That also applies to the flywheel mounts on the upper, lower, and magwell