Probably the best Mac drive cloning/backup utility:
http://www.shirt-pocket.com/SuperDuper/
Also useful if you don't have access to a backup boot drive:
http://applejack.sourceforge.net/#top
You need to be booted from another drive to repair your internal drive with Disk Utility (Applications>Utilities), but you can repair permissions on the boot drive which is a start.
Also check the general troubleshooting thread at the top of the forum for Pro Tools specific suggestions.