How to restore a backup copy of 'My Music", from an external backup system

Is there a document somewhere on the procedure to recover iTunes when you used a 3rd party backup system?
Issue: I am having difficulty restoring my iTunes library from a third party backup system that mirrors all the files on my computer onto a remote disk drive. First I restored the files onto a new computer, then I loaded iTunes
for windows, and then used authorize option. iTunes does not show any of my files, and appears to have erased the files I restored. I am lost what to do next, I can restore the files again if need be, just want to read some instructions instead of guessing.
Background: My desktop computer gave me error messages when I rebooted my computer just after upgrading from iTunes 7.0.18 to iTunes 7.0.2. I got an error message that the operating systems SMS hive file is corrupt (a security file). After some investigation a technical person in my company tol me that the file is gone, on both my mirrored disk drives. Would appear that this is a serious iTunes bug or a serious hardware problem. Not knowing which, and confident I have a good backup, I have placed that computer on the side, and took a spare PC and started configuring it to be my new home computer.
I loaded all the Windows patches and installed, recovered all the files under "My Documents", loaded iTunes, Authorized the computer, and don't see my files. When I go back to "My Music" subdirectory I see very few files, when I am in iTunes I don't see my music.
The backup and restore was for all the files in "My Documents" kept on a remote server in my home, a Seagate Technology product called Mirra.
Questions:
1. How should I have restored those files? Apparently the method I choose does not work. All Apple FAQ information is based on me using the Apple Backup & Restore method, which I don't use, instead favoring using a single product to backup all my data.
2. Are there other reports of microsoft Windows Hive or SMS files being damaged in the iTunes upgrade process? Any thoughts as to this being related to the iTunes upgrade process or digital rights management?

First -- by default iTunes stores its Library in "My Documents\My Music\iTunes\iTunes Library.itl", and its Music in "My Documents\My Music\iTunes\iTunes Music\".
Make sure you have a "iTunes Library.itl" after the restore -- if not, and your backup software supports it, try an older version of the file. If your backup software only keeps the last version of the file -- well, then you are SOL, and you will have to re-add the files to the Library. You will also have to rebuild your playlists, ratings, etc.
Since you have "very few files" in the iTunes Music directory -- either you weren't storing your music there, or your backup didn't work. Are you sure you weren't using a non-default location for your music files?
If you had a hardware problem then it is likely that your backup stopped working properly at some point. This is why you need a rotating backup scheme and periodic archiving of files to non-writeable media (If you have the time/money)

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