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.
Don't worry. Your question are appreciated as with such good feedback I will learn a lot too.
Now this is a bit more complicated. What speed you set in software you use to control the printer and what are the values you set in firmware?
My working values are around 4mm/s (240mm/min) for maximal extrusion speed and 17mm/s^2 for acceleration and retraction. With 1/16 microstepping I have 7026.994 microsteps/mm on extruder. You will probably have slightly different number as my hobbed bolt diameter is around 6mm. With shallower groove it may closer to 6000 microsteps/mm.
Also check my conversation with Eddiie: http://www.thingiverse.com/thing:945156/#comment-1191875, where are some more things explained. (you will have to copy paste the link)