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.
If you get some of that stuff concepted out, please upload it as a remix. Your ideas sound interesting and it'd be cool to see people iterate on this. It would also be nice for there to be my version of the kit where it's print everything as one piece, and another version of the kit that's more usable for people with beds smaller than 300x300mm.
For attaching the rails, the V2 I'm working on (it's taking a while because my printer is on the fritz most days) uses M4 screws with nuts sunk into the body, so that will clean up and reinforce the rail installation a bit. The V2 has slightly different body geometry but the concept would carry over to this version just fine, and will eventually get implemented when I have the time.