Restore from time capsule not working

Like many others I received this email last week:
Dear iMac owner,
Apple has determined that certain 1TB Seagate hard drives used in 21.5-inch and 27-inch iMac systems may fail. These systems were sold between October 2009 and July 2011.
My imac is backed up every day to my time capsule. When they replaced my hard drive they suggested that since I was using time capsule that i do a complete restore and not copy info from my old hard drive since there was a problem  with it. After doing a complete restore I find there are many applications that did not get restored, like iPhoto, Microsoft Excel, Word, Outlook, Photoshop, and many others. I can see individual photos that are in iPhoto, just not the application. When I go into time machine I see none of these programs. Needless to say I am in near panic mode, having no idea how this could happen or how I can get them reinstalled. Your suggestions are greatly appreciated.
Gary in Oregon

You can erase & install the system again, and when finished migrate your data within the setup assistant from the backup volume. With this method the system files are installed fresh from disc and not transferred from the backup.

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