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After a lot of faffing about, and yet another factory reset, I finally got calibre talking to the Kobo.
What I think the issue is that the SD card and the main memory MUST be ejected simultaneously otherwise you get the not ejected correctly error which seems to damage something on the Kobo. So, the workaround is to go to Finder, select both the Kobo and the SD card drives using Cmd, right click and select Eject. Then you can safely disconnect the Kobo.
Fingers crossed, that will prevent further problems (although I'm leaning to a replacement device with a bigger on board memory as it's possible the battery is on the way out anyway).
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