If you still think you might have a rootkit, wipe your system clean. It's really the only surefire way to get rid of a rootkit.
I think after a disaster like this the only secure method is to reinstall all affected computers, make some images of the harddisk so you can still analyze what happend.
+1, don't try to fix a os if you think it might have a root kit.
Root kit cleaners are like anti virus software, they only clean what they know and recognize ....
Very true, which is why I don't necessarily condone Rootkit removers. I'd much rather lose everything on a hard disk than have my BTC get stolen (again in his case).