Time Machine Problem with Apple Programs after Restore from A&I

Ok here is my situation. I originally did an Archive and Install before Installing Leopard. I was having performance issues with Photobooth and Time Machine. So, I decided to back everything up and do an Full Restore from Time Machine. I resotred from the Utility menu within the Leopard boot disc. However, after the restore ALL of my Apple programs were missing from Finder and the Dock. Including mail,itunes,photobooth,keynote etc..All iwork,ilife and everything else that came pre bundled. Now, I did an install of Leopard after the Restore (upgrade) and I got the basic apps back. My question now is where my other apps are hiding?? Are they somewhere within the previous system folder from the original Archive and Install?? (I havent been able to check because i'm now at work when the possibility dawned on me)
Does anyone know where these programs would be and how I can restore them?
Also, my prebundled software (Final Cut Express HD) that came pre bundled with My imac G5 originally is asking for a product serial number before it can launch. However, i never had a serial key for it.
Can someone please help and shed some light on this situation.

Additional Info:
Imac G5
1Gb Ram
Original Install was Archive and Install
Did Full Backup With Time Machine
Restore Under Utility in Leopard Boot Disc
All Apple programs were missing
Did an Upgrade>Install of Leopard after Restore and got back the basic Apps like mail, Garage Band, iTunes etc... However, all iLife was gone as well as Soundtrack and iwork 08...not to mention my Final Cut Express HD now wants a serial # that I do not have because it was pre installed originally with the iMac G5
Where did these programs go?
How do I get them to restore?
fyi-- My dock where the programs were located (in addition to Applications folder) just had a bunch of ? marks on it where the icons would usually be.
Is it a result of the Archive and Install and the Applications are in the previous system folder?
I cant figure it out because when I search for the programs in FInder all I find is files for the programs and cache files etc... But not the actual Application icon

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