How do I install a new system file to replace the damaged one

I am tring to repair the permissions on my computer and am getting all of these types of errors. Computer is dragging. I reinstalled my operating system and this is what is happening. Any suggestions. Happening on my desk top I Mac and on my Mac Book. I did google search and Error 23 is "These errors indicate that the Mac tried to access one of the standard routines in the system file and couldn't find it. In all probability, that means you have a corrupted system file. Try installing a new system file to replace the damaged one."
Here is a sample of what disk utilities says
Open error 23: "Too many open files in system" on System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8/doc /activesupport-2.3.5/ri/ActiveSupport/CoreExtensions/Array/Conversions/cdesc-Con versions.yaml
Open error 23: "Too many open files in system" on System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8/doc /activesupport-2.3.5/ri/ActiveSupport/CoreExtensions/Array/Conversions/to_format ted_s-i.yaml
Open error 23: "Too many open files in system" on System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8/doc /activesupport-2.3.5/ri/ActiveSupport/CoreExtensions/Array/Conversions/to_param- i.yaml
Open error 23: "Too many open files in system" on System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8/doc /activesupport-2.3.5/ri/ActiveSupport/CoreExtensions/Array/Conversions/to_query- i.yaml
Open error 23: "Too many open files in system" on System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8/doc /activesupport-2.3.5/ri/ActiveSupport/CoreExtensions/Array/Conversions/to_senten ce-i.yaml
Open error 23: "Too many open files in system" on System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8/doc /activesupport-2.3.5/ri/ActiveSupport/CoreExtensions/Array/Conversions/to_xml-i. yaml
Open error 23: "Too many open files in system" on System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8/doc /activesupport-2.3.5/ri/ActiveSupport/CoreExtensions/Array/ExtractOptions
Open error 23: "Too many open files in system" on System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8/doc /activesupport-2.3.5/ri/ActiveSupport/CoreExtensions/Array/ExtractOptions/cdesc- ExtractOptions.yaml"
It says it should be done in 6 minutes and I am going on hours!
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_TW.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_TW.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/zh_TW.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/zh_TW.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/zh_TW.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/zh_TW.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_CN.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_CN.lproj/UIAgent.nib"."
Any suggestions?

I would apply or reapply the 10.6.8. Combo Update from Safe Boot (hold Shift down at startup -- give it much more time to boot than usual and leave it in SB for a few minutes before doing anything.)
http://support.apple.com/kb/dl1399
The messages you are seeing beginning with "Permissions differ on...." can be ignored.

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