ITunes losing settings after reinstall

My HDD failed and I had to reinstall Windows. Before it failed I was briefly access the drive and copy the bulk of the App Data folder.
Now that I've reinstalled Windows (Vista Ultimate x64) and reintalled iTunes, I copied the Apple & Apple Computer folders back into the Local & Roaming sections of AppData for my user account, but iTunes doesn't seem to be getting it. It's lost the vast majority of my album artwork (I did at one point go through and manually add artwork for a large number of albums). Also when I tell it to sync my iPhone, it says that it's going to wipe out the phone and copy music from the computer instead.
There has to be a fix for this. Thoughts?

+copy the bulk of the App Data folder.+
Unfortunately, this wasn't the most important folder, as far as iTunes is concerned.
You should have gotten the /My Music/iTunes folder and all its subfolders, instead.

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