A (hopefully) really strong part that can be mounted to the holes currently holding the Y motor and move the Y motor up to mount on this part outside the case and directly drive the Y rod with a shaft coupler (and longer Y rod). The idea is to utterly eliminate backlash.
I've replaced some files with a new version I was able to successfully print. You can follow progress at http://tomhorsley.com/hardware/solidoodle/solidoodle-ydirect.html
I've now updated the files again with tweaked openscad code that produces a model slic3r likes. No need to run it through netfabb repair any longer.
And now I've successfully printed a test cylinder and all traces of backlash seem to be gone, so I'm calling this completed.