Hard drive died - multiple problems with backed up home folder

My friend called me when she started having some problems with her home iMac. After we did went through a myriad of troubleshooting items, I determined that her hard drive was failing and suggested she backup her home folder immediately to another drive. She copied her home folder over to her old Mac and took the iMac into the Apple Store for further diagnostics. Sure enough, her hard drive had failed and they replaced it for her.
She reinstalled Leopard and set it up with a new account. We tried using the Migration Assistant to copy her old home folder back over but because she copied it rather than using Time Machine, Migration Assistant doesn't see it as a viable home folder. I'm very comfortable using the Terminal since I support both Macs and Linux in my department so I logged in as root and copied over her folders to the new account. That generally worked but we now have a ton of permissions problems of which Disk Utility doesn't fix. I'd like to start fresh again from her backed up home folder. So my question is if I can't use Migration Assistant to move over her old home folder, how do you make OS X see her old home folder as a viable account? (I hope this makes sense.)
Thanks in advance!

I would suggest the following.
make a new temp admin account and get rid of the new account she made already. log in as the temp user and copy the old home folder from the external to /Users. then go to system preferences->accounts and make a new account with the same short user name as the name of her old home folder. It will say that a home directory by that name already exists and ask if you want to use it. say "yes". this should recreate that user and take care of all permissions issues.

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