I replaced my primary hard drive. Time Machine restore didn't work. HELP!

My 320GB hard drive that came with the mac pro was out of room. I got a new 1T, put it in, formatted the drive, told Time Machine to restore, it did, the information is there....
BUT, Almost nothing is working. If i click on a program to open (mail, itunes, etc.) the crash window pops up. The info is there but it seems no one is talking to each other inside. Funny thing is that "preview" and "viewer" programs do work, just nothing else. Any ideas????
Thanks a million...

Don't panic. Let's re-prep the new drive a little differently. This will add considerable time to the formatting process. Again, I'm assuming you have booted the computer from your old hard drive.
Extended Hard Drive Preparation
1. Open Disk Utility in your Utilities folder.
2. After DU loads select your hard drive (this is the entry with the mfgr.'s ID and size) from the left side list. Note the SMART status of the drive in DU's status area. If it does not say "Verified" then the drive is failing or has failed and will need replacing. SMART info will not be reported on external drives. Otherwise, click on the Partition tab in the DU main window.
3. Under the Volume Scheme heading set the number of partitions from the drop down menu to one. Set the format type to Mac OS Extended (Journaled.) Click on the Options button, set the partition scheme to GUID then click on the OK button. Click on the Partition button and wait until the process has completed.
4. Select the volume you just created (this is the sub-entry under the drive entry) from the left side list. Click on the Erase tab in the DU main window.
5. Set the format type to Mac OS Extended (Journaled.) Click on the Options button, check the button for Zero Data and click on OK to return to the Erase window.
6. Click on the Erase button. The format process can take up to several hours depending upon the drive size.
Please be sure you read the above instructions carefully before proceeding to be sure you don't miss anything such as selecting the GUID partition scheme.
I will also suggest, just for precautionary reasons, that you do the following before cloning your old drive to the new drive:
Repairing the Hard Drive and Permissions
Boot from your Snow Leopard Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Utilities menu. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list. In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive. If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer. Now restart normally.
If DU reports errors it cannot fix, then you will need Disk Warrior and/or Tech Tool Pro to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.

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