Installing Network Link Conditioner for All Users (Yosemite)
Solution 1:
Ran into the exact same problem. Installed the Network Link Conditioner when my system had OSX Lion and XCode 4 or 5. Great tool but did not need it again until today. Found it no longer worked. My system now has OSX Yosemite and XCode 6.4 so I downloaded Hardware IO Tools for Xcode 6.3. Got the same message about not being able to replace it since it was installed together with OSX.
My solution was to first drag the tool from the opened .dmg onto the desktop and to then manually replace the tool using the command line:
cd Desktop
sudo mv /Library/PreferencePanes/Network\ Link\ Conditioner.prefPane Network\ Link\ Conditioner.prefPane.old
sudo cp -r Network\ Link\ Conditioner.prefPane /Library/PreferencePanes/
Solution 2:
I actually figured out what I did wrong and I wanted to record it in case anyone else ran into this issue.
The key for a setup like this is not to try and install it from anywhere but the Hardware IO Tool disk image. As soon as I did that, everything worked perfectly.
Previously, I had yanked the PreferencePane and deployed it with ARD, telling it to inherit the permissions of the root folder...and I'm pretty sure that's what messed it up.
Solution 3:
Here is a more easy way. You can [option + right click] the icon in the System Preferences. Than click the "Remove the 'xxxx'" item. After that, just click the "Network Link Conditioner.prefPane" to install.