Not basic questions at all.
Shared preferences are just that -- shared -- as long as they're "user" preferences and not "system" preferences. For example, bluetooth pairings are "system" preferences and aren't shared. Your login items are "user" preferences.
Tiger is a bit different than previous OS releases in that they changed the way some data is stored. Mail is radically different, as are iCal and iSync. Because of this, you need to be more careful when rolling back.
I've detailed this in the "Tiger Compatibility" post in the FAQ, so take a look there.
Once you're done testing on the Safety Clone, you'll just boot back to the 'real' drive and upgrade it to Tiger.
The Music App needed to be re-registered because it's way WAY too restrictive -- a common feature of this kind of protection. (Locking to drives is really dumb, as the drive is the one thing that tends to fail.) But, it's hard to say what'll happen on the original, since I don't know where the activation preference is stored. You'll just have to try it...
Hope that offers a small amount of help, at least!
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--Dave Nanian
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