You can't use a back up with no data and only structure. This is why you get the datastore error.
It sounds like you need to start over with this upgrade. Do your database using ssh if possible and use it to import as well. Then upload your fresh files over the old ones on your test site ofcourse and try again. Do the whole upgrade though at once and not in steps. I mean I know it goes through steps but go to completion.
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