I am attempting to fix a system wherein there some major permissions issues. Running the repair permissions tool in disk utility does not fix them. The machine in question is having issues saving files and preferences and has run into a number of programs that don't work correctly. Background is below, but if you have any suggestions, Bash scripts, programs, etc. that can help fix this issue, I'd be very grateful. This all started when the owner tried to delete a portion of Integro's Virus Barrier X. Their system refused to boot afterward. I was able to mount the computer in target disk mode, so I tried to backup as much as I could onto an external drive; only, I was told I didn't have permission to copy the files. An apple support rep confirmed my suspicion that the only way to deal with this would be to either go through and manually track down the file or do a global "apply to enclosed items" permissions change to the problem areas. Knowing it was probably a bad idea, I tried my best to avoid this, but there didn't seem to be another way. After backing up, I performed a reinstall from the recovery disk and Lion boots fine, but I am now having the issues above.