missing or corrupt system file

Friday I ran CCleaner to remove temp files and to clean the registry. I made a registry backup on the desktop then proceeded with the cleaning. All went well as usual but this time when I tried to restart the computer, I am now receiving the error message -- windows could not start because the following file is missing or corrupt: windows\system32\config\system -- Computer is a Dell Dimension 4550 running Windows XP Professional. I do not have the original XP Pro CD's. I have been able to go online and create a set of XP Pro Setup/Recovery floppies to boot the system. If I select "R" to attempt to recover the system file will this set the system to the new state as far as software is concerned? Is there a better approach that will save current software and data. Not sure where to go from here, any help would be greatly appreciated. :unsure: