It sounds, CJ, like you didn't use "Backup - all files" as your copy script. Instead, it seems that you used "Safety Clone" which -- as it says in the WGTH? section and in the User's Guide -- shares both your user files and most applications with the original drive. They're never copied, as the Safety Clone isn't a backup: that's why your backup doesn't have them.
Your user files should still be on your eMac's drive. Do you have Disk Warrior or anything similar that would let you repair the drive?
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--Dave Nanian
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