Leopard Crashing, Can't Restore Previous Settings

I have a major problem with Leopard on my MBP. When I went to start up this morning, I got stuck on the initial gray screen with the apple logo -- it wouldn't get past that screen, icon was just spinning, etc. I have a SuperDuper back-up that was fairly recent (2 days ago), and I went to start-up using my back-up (which is an external usb 2.0 disk). The MBP started up from the back up, but the desktop was all changed -- it looks like it's the original Leopard desktop -- purple space screen and all the original dock icons (which I had substantially changed). It appears that my user files were all available on the backup disk, but all kind of strange things happened when I went to use programs. For instance, when I went to use Spotlight (off of the backup disk), nothing was indexed (it had been previously). When I went to start Entourage, I got an error message (-5000) saying it couldn't open that identity. So I figured I had a major permissions problem. But when I tried to repair permissions (again, on the backup disk), I got an error message.
So I'm a little baffled about what exactly has gotten messed up. I'm keeping my fingers crossed that, since I have a very recent backup, I should be able to restore things one way or another without too much loss. But does anyone have any suggestions about what to do?
I tried restoring the hard disk on the MBP using SuperDuper, and that gets the MBP to the point where it can start up, but the above problems still remain -- i.e., very strange behavior. Could this be a hardware problem, and if so, how do I find that out?
Sorry I'm so all over the place with this, but that's part of the problem -- I can't quite figure out what's going on.
Any help would be greatly appreciated.

You can try to restore a previous version of the sessionstore.js file.
*Right-click: Properties > Previous Versions
*http://windows.microsoft.com/en-US/windows7/Previous-versions-of-files-frequently-asked-questions
You can use this button to go to the Firefox profile folder:
*Help > Troubleshooting Information > Profile Directory: Show Folder (Linux: Open Directory; Mac: Show in Finder)
*http://kb.mozillazine.org/Profile_folder_-_Firefox

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