That largely sounds like the problem described
here. That problem does survive a factory reset. The fix for that is to restore an image to the internal micro SD card. I have sent you a PM with a link to the image.
But, the calibre issue is different. We would need to see the error details to have an idea of what that part of the problem is. I'm not sure about the rest.
I would say the thing to do is to restore the image, possibly to a new card, and see what happens. There is a good chance that the rest of the issues were side-effects of the main one.