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.
I ended up just making long hexagonal shafts that fit the M4 nut perfectly. It's easy enough to seat them, though it's probably impossible to get them out without damaging the model, so they would be committed to the project until the person who prints it is "done" with it I suppose.
I was gonna ask if you would be okay with me adding changes you make to the master file, but didn't want to presume. If/when you get the changes you're thinking about done, shoot me a DM and I'll send you an email address to send them to (thingiverse is weird with file attachments ime). Otherwise just post it as a remix, I'm fine with it either way. Thanks!