Fixing Permissions (iTunes.app) in OS 10.8.5 Update - HELP FIX?

I recently updated from OS 10.8.4 to OS 10.8.5 .... and although the update went fine, I have seen an issue with the "Apple Disc Utility" that raises concerns for me.
Everytime I have run the "permissions" repair, I have seen a "TON" of repair lines for the "Applications > iTunes.app > Contents . Resources > files.
The list must have been a hundred lines or more ...
(Actually were too many to screen grab, so here are a few I see):
Any idea why these "iTunes" permissions keep poping up to be fixed .... and then once fixed or repaired, just keep popping up again to need "permissions" repair again in the "Apple Disc Utility"?
Also, the first repair "permissions line I see is always:
> Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified abd WILL NOT BE REPAIRED
Any idea as to what this is refering too as well.
I never had any problem repairing "permissions" before this OS 10.8.5 update .... and certainly not to the enormous length that the "permissions" repair liting shows. It's a huge list of over 100 iTunes permissions that need "permissions" repaired.
Any help will be appreciated ....

This is what I keep running into when trying to delete (or install new) the iTunes app from/to my HD Applications folder:
I have been having Apple "permission" repair issues with the newer OS10.8.5 update, and want to re-install my previous iTunes version (v11.0.4 or 11.0.5). When I try to remove the existing 11.1.4 version (that has the permission repair issues), I am not allowed to simply place the 11.1.4 app in the trash and delete, as I get the following pop-up window:
When I also try to launch the iTunes 11.0.5 installer package, I then get this:
How do I get around these issues and delete my iTunes 11.1.4, so I can then install the previous iTunes 11.0.4 or 11.0.5.

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