Hi Ben,
I think the above error was due to the elements not being configured at all despite being enabled. In my experience the sync only displays warnings for missing CSV files if elements are enabled and set to look for CSV files, but it should run perfectly.
Does the user you wish to update already exist in the system? My first suggestion would be to double-check if all the Id-Numbers are correct.
Are there entries for your sync in the Sync log?
Regards,
Tobias