How can I tell if CCleaner affected my computer negatively and how do I restore to settings before application?

1) Your pc no longer boots up
2) Your pc is on fire
3) Your pc has melted
4) Oh, I dunno, one or more of the countless idiosyncrasies or foibles of your pc no longer acts as it did before.

There's no way you can restore your pc settings after using CC, except for the registry clean. Assuming you ran a backup when prompted, then right click on the saved .reg file and select merge.