For those who have read the posts on System Restore failed, but are running Windows 8.x, I also found a solution for my registry problem.

When running Windows 8.1 x64 a copy of the registry information is saved in c:\windows\system32\config\RegBack so you can make a copy of these registry files to your c:\windows\system32\config directory and that solved the issue I had of Windows 8.1 not starting up correctly after some modfication had been made manually to my registry (while using the PC Tune-Up application).

Success !