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.
A great low coast way to acquire 8mm smooth rods is from old flatbed scanners or printers. The scanner I took apart had two 17" (~420mm) rods, and most HP printers have 8mm rods that are at least 14" (~200mm). Also, the stepper motors used in most scanners could be (theoretically) be used as an upgrade from the 28byj motors, but I have yet to test mine.
I couldn't find a 3mm threaded rod for the Z axis endstop, so I used a wood screw instead. It is harder to adjust, but it works OK.