Damaged system icons, how do I restore them?

I recently bought a new MacBook Pro Retina display and have been installing applications and copying over old files to start with a fresh system. I think I may have tweaked the default system icons because they look a little wierd:
I have been playing around with Onyx, TinkerTool, and Default Folder X. I'm not sure if they had anything to do with the wierd icons or not. Everything was fine for a few days. Affected icons are in default Apple apps and 3rd party apps. Not every icon is messed up, but many are.
I'm trying to restore them, but haven't had any luck yet. Has anyone seen this before and do you have a solution?
Mark O.

I made a couple of attempts to reinstall Lion. These attempts were done by restarting and holding command-r during boot up. Not wanting to lose the information I had already added to my computer I did a restore from a time machine backup I made. Apparently this didn't touch Lion, it just re-installed my information and settings. The icon problem persisted.
On a second attempt I decided I would try to do a clean install of Lion and figure out how to get my infomation back later. After the restart and holding command-r again my mac went into internet recovery mode. It downloaded some 4GB of data from Apple, but I'm not sure what that did. I think it downloaded OS X Lion. It then re-installed the OS. I was surprised when it came back to the login screen - it seemed that nothing had changed. Upon logging in I found that my information was still there, but the icon issue was fixed. I don't know if it installed Lion without disturbing my stuff, or if it did a clean install and then restored my info from the time machine backup. It didn't take more than an hour, hour and a half.
In any case, all is well now. I still don't know what messed up my icons, but at least it can be fixed without too much trouble. I'm glad I'm on a mac. This would have caused headaches on Windows since it lacks native backup and restore features.
Mark O.

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