How to set all file permissions to default?

Question

So a few background notes are in order. I came across an article on the NSA's website titled Hardening Tips for Mac OS x 10.6 "Snow Leopard", needless to say I have come to believe I have made this irreversible. The NSA suggested to do some fancy command line coding to disable this, modify that, and change permissions to this. After hours spent on "hardening" my system, I have little hair left to pull in frustration. Is there any way to restore all file permissions back to default? I have used the Repair Disk Permissions, but that has done very little. To give the scope of what permissions have been skewed, I have observed several things:
The desktop wallpapers, on all Desktops (as I'm in Lion 10.7.3), start from the same picture every time. I have the wallpapers changing, randomly, every 5 minutes.
Safari doesn't keep the home page. No matter how often I try to change the homepage, I restart Safari, and I'm right back to the original homepage.
Firefox doesn't retain the fact that I want it to be the default Web Browser. In fact, it keeps "forgetting" that I've used it before, and thus brings me to their awesome start page whenever someone first uses Firefox.
Spotlight gets "stuck" i.e. almost every time I start my machine, it indexes. Even after I let it finish indexing, the next time I start my computer, it starts again.
I have to input the administrator password after almost every activity, such as copying to the desktop, moving an application not bought from the Mac App Store into the /Applications folder, deleting a file from anywhere inside my home folder, etc.
Some preference panes that need access to certain folders, such as Hazel's access to my desktop, are denied that access without ever prompting me for a password (though even if it did, it would get rather annoying after every startup)
My firewall (in System Preferences>Security & Privacy>Firewall) doesn't "remember" that I do indeed want Dropbox to accept incoming connections. I have to input my admin password at each startup after clicking "allow"
Opera pretty much doesn't function. Its bookmarking capability, home page, saved tabs, any thing that requires the saving of any type of preference to the computer results in a dialog pop up informing me that Opera failed to save what it needed, and prompts me to "Try again" or "Cancel" (hint: the "Try again" button doesn't work)
There are more symptoms of an ever growing problem.
I have backed up my machine from Time Machine, but I think it retains these file permissions, unless I'm wrong.
Summary:
How can I fully restore EVERY file permission back to default? Repair Disk Permissions doesn't work
Is there a way that I can re-install Mac OS X, restore through Time Machine, and achieve the default file permissions, essentially losing all file permissions?

Answer 1

Repairing the permissions of a home folder in Lion is a complicated procedure. I don’t know of a simpler one that always works.
Launch the Terminal application by entering the first few letters of its name into a Spotlight search. Drag or copy – do not type – the following line into the window, then press return:
chmod -R -N ~
If you get an error message about permissions, enter this:
sudo !!
You'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning not to screw up.
Next, boot from your recovery partition by holding down the key combination command-R at startup. Release the keys when you see a gray screen with a spinning dial.
When the recovery desktop appears, select Utilities ▹ Terminal from the menu bar.
In the Terminal window, enter “resetpassword” (without the quotes) and press return. A Reset Password window opens.
Select your boot volume if not already selected.
Select your username from the menu labeled Select the user account if not already selected.
Under Reset Home Directory Permissions and ACLs, click the Reset button.
Select  ▹ Restart from the menu bar.