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.
Heading to work in a few minutes so I don't have time to go over the whole project till tonight, but I wanted to point out one thing. You talk about it not being 'self replicating" because it cannot print rails that are larger than it's existing build volume. This isn't as much of a problem as you make it out to be. If the rails are printed in ABS they can easily be glued together. ABS solvent welds things as strong as if they were the same piece.
Of course there are several other reasons it's not "self replicating" but I wanted to point out that build volume doesn't have to be an excuse.