Atualizando o PC
Você já fez as etapas básicas de solução de problemas, mas parece que o sistema ficou seriamente confuso. Considere fazer uma atualização do sistema:
If your PC isn't performing as well as it once did, and you don't know why, you can refresh your PC without deleting any of your personal files or changing your settings.
Note
If you upgraded your PC from Windows 8 to Windows 8.1 and your PC has a Windows 8 recovery partition, refreshing your PC will restore Windows 8. You’ll need to upgrade to Windows 8.1 after the refresh has finished.
Warning
Apps you installed from websites and DVDs will be removed. Apps that came with your PC and apps you installed from the Windows Store will be reinstalled. Windows puts a list of removed apps on your desktop after refreshing your PC.
To refresh your PC
Swipe in from the right edge of the screen, tap Settings, and then tap Change PC settings. (If you're using a mouse, point to the upper-right corner of the screen, move the mouse pointer down, click Settings, and then click Change PC settings.)
Tap or click Update and recovery, and then tap or click Recovery.
Under Refresh your PC without affecting your files, tap or click Get started.
Follow the instructions on the screen.
Leitura adicional
Registro do Windows
O registro não precisa ser limpo. Evite usar esses "otimizadores", porque eles podem fazer mais mal do que bem, como você percebeu.
The Windows registry is a database that lists all of the configuration settings that determine how Windows looks and behaves. Sometimes, settings that are no longer needed will remain in the registry in case they're ever needed again. There's nothing unusual about this, and this data is small in size.
[...] Although a registry setting can become corrupt on occasion, in general, the registry is self-sufficient.
Source: Are registry cleaners necessary?