Since you have used that registry cleaner you should let it's maker help you. The forum moderators here all seem to be of the same mind here. Not on cares if it's 5 stars. It's a cause of issues and not a cure so trying to undo all the bad things I've seen with a discussion here is fruitless.
We know that malware and rootkits along with what you used can break both SFC and SR.
And from my discussions so far we reload the OS when it gets that broke.