I restored from time machine but lost all my preferences

Question

I have a late 2008 Mac Pro 2 x 2.8GHz quad core running Mountain Lion.
I have been using the 500Gig HD as my Startup Volume that came with the computer.  This drive got too full so I am upgrading to a 3TB drive that I partitioned into 1TB for my startup volume and the other 2TB for other stuff.
Using SuperDuper, I made an exact copy (at least I thought so) of my 500Gig startup volume onto the new 1TB partition.  After doing so I swapped out the 500Gig for the 3TB and re-started the computer.  Computer boots fine and all the files are there but here are the PROBLEMS:
-None of my settings and preferences are working.  My desktop, dock and settings are default.
-Under my user, most of my folders said "The folder can’t be opened because you don’t have permission to see its contents. mac pro."  I circumvented this by going to the "get info" and turning on my permissions, but it is still wierd.
-When I go to open my programs (eg Microsoft word) it welcomes me as if it is a new install and I am given a prompt to enter my serial number.
Sooooo, I tried another route, went to my backup drive, (I have another drive that has time machine of the 500 gig startup volume saved to it) and used time machine to "restore" a backup of my 500Gig startup volume onto the new 1TB partition.  After doing so and restarting, guess what.  No changes; all the same problems.
HELP!!!
Thanks.

Answer 1

This procedure will unlock all your user files (not system files) and reset their ownership and access-control lists to the default. If you've set special values for those attributes on any of your files, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it.
Step 1
If you have more than one user account, and the one in question is not an administrator account, then temporarily promote it to administrator status in the Users & Groups preference pane. To do that, unlock the preference pane using the credentials of an administrator, check the box marked Allow user to administer this computer, then reboot. You can demote the problem account back to standard status when this step has been completed.
Triple-click the following line on this page to select it. Copy the selected text to the Clipboard (command-C):
{ sudo chflags -R nouchg,nouappnd ~ $TMPDIR.. ; sudo chown -R $UID:staff ~ $_ ; sudo chmod -R u+rwX ~ $_ ; chmod -R -N ~ $_ ; } 2> /dev/null
Launch the Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.
Paste into the Terminal window (command-V). You'll be prompted for your login password. Nothing will be displayed when you type it. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The command will take a noticeable amount of time to run. Wait for a new line ending in a dollar sign (“$”) to appear, then quit Terminal.
Step 2 (optional)
Take this step only if you have trouble with Step 1 or if it doesn't solve the problem.
Boot into Recovery. When the OS X Utilities screen appears, select
Utilities ▹ Terminal
from the menu bar. A Terminal window will open.
In the Terminal window, type this:
res
Press the tab key. The partial command you typed will automatically be completed to this:
resetpassword
Press return. A Reset Password window will open. You’re not  going to reset a password.
Select your boot volume ("Macintosh HD," unless you gave it a different name) 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.