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.
Thanks for posting pictures! I'm really happy we found a solution.
Just be careful with nylon nuts. They will help with friction, but as every plastics parts they will wear off after some time. Don't have personal experience with them, so can't tell how soon it will come and it will also depend on precision and smoothness of the thread on the M5 rods. If normal nuts are working for you now, there is probably no reason to change them any more because you probably hit the limit of your motors. But if you would like to experiment, I will be happy to hear about the results you achieved.