Updating broke the website and restoring did not fix it..

I was updating from 0.64 to 0.78 and it broke everything.. only got 500's

So I used the restore method to revert, but that could not fix it.. here is the logging of the restore:

[05/10/2016 07:56:50 > c6198c: SYS INFO] Status changed to Initializing
[05/10/2016 07:56:50 > c6198c: SYS INFO] Run script 'restoreBackup.ps1' with script host - 'PowerShellScriptHost'
[05/10/2016 07:56:50 > c6198c: SYS INFO] Status changed to Running
[05/10/2016 07:56:51 > c6198c: INFO] Restoring Full Site Backup
[05/10/2016 08:04:09 > c6198c: ERR ] Remove-Item : Directory D:\home\site\wwwroot cannot be removed because it is
[05/10/2016 08:04:09 > c6198c: ERR ] not empty.
[05/10/2016 08:04:09 > c6198c: ERR ] At D:\local\Temp\jobs\triggered\restoreBackup.ps1\ly0vatuz.xzt\restoreBackup.ps
[05/10/2016 08:04:09 > c6198c: ERR ] 1:6 char:5
[05/10/2016 08:04:09 > c6198c: ERR ] + Remove-Item -Path ./wwwroot -Recurse
[05/10/2016 08:04:09 > c6198c: ERR ] + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[05/10/2016 08:04:09 > c6198c: ERR ] + CategoryInfo : WriteError: (D:\home\site\wwwroot:DirectoryInfo)
[05/10/2016 08:04:09 > c6198c: INFO] All done
[05/10/2016 08:04:09 > c6198c: ERR ] [Remove-Item], IOException
[05/10/2016 08:04:09 > c6198c: ERR ] + FullyQualifiedErrorId : DirectoryNotEmpty,Microsoft.PowerShell.Commands.
[05/10/2016 08:04:09 > c6198c: ERR ] RemoveItemCommand
[05/10/2016 08:04:09 > c6198c: ERR ]
[05/10/2016 08:04:09 > c6198c: ERR ] Rename-Item : The process cannot access the file because it is being used by
[05/10/2016 08:04:09 > c6198c: ERR ] another process.
[05/10/2016 08:04:09 > c6198c: ERR ] At D:\local\Temp\jobs\triggered\restoreBackup.ps1\ly0vatuz.xzt\restoreBackup.ps
[05/10/2016 08:04:09 > c6198c: ERR ] 1:7 char:5
[05/10/2016 08:04:09 > c6198c: ERR ] + Rename-Item D:\home\site\wwwroot-backup wwwroot
[05/10/2016 08:04:09 > c6198c: ERR ] + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[05/10/2016 08:04:09 > c6198c: ERR ] + CategoryInfo : WriteError: (D:\home\site\wwwroot-backup:String)
[05/10/2016 08:04:09 > c6198c: ERR ] [Rename-Item], IOException
[05/10/2016 08:04:09 > c6198c: ERR ] + FullyQualifiedErrorId : RenameItemIOError,Microsoft.PowerShell.Commands.
[05/10/2016 08:04:09 > c6198c: ERR ] RenameItemCommand
[05/10/2016 08:04:09 > c6198c: ERR ]
[05/10/2016 08:04:09 > c6198c: SYS INFO] Status changed to Success