Super Clean re-install Question

I have a Mac Pro 8 core tower with several internal hard drives.
The one called Macintosh HD that came with it has been upgraded all the way since prior computers, migrations, etc.
A newer 1TB drive was installed and a fresh OSX made it a bootable drive. When it was upgraded to Snow Leopard, it showed some "issues" that screwed up Photoshop and no amount of re-installing OSX SL or Photoshop itself could fix the problem.
Other programs fail on both boot drives. In particular iMovie 09's update to v 8.0.5. The iMovie 09 from the iLife disks runs okay, but if updated, it fails big time on both bootable drives. Version 8.0 runs, but v 8.0.5 won't even boot on either drive.
So,
I want to install a virgin OS X Snow Leopard on one drive, reinstalling its programs and data from back up sources. I backed it up with SuperDuper and Time Machine, both, so I should be able to do that.
What's the best strategy? I don't want to bring across the System from backups, covering the virgin one I just installed, but I would like to be able to bring back Apps without going through infinite serial numbers, etc.

What's the best strategy? I don't want to bring across the System from backups, covering the virgin one I just installed, but I would like to be able to bring back Apps without going through infinite serial numbers, etc.
That's not really going to be possible. Any applications that involved an installer (rather than just drag and drop into the Applications folder) will have files scattered around in numerous other places, and unless you know precisely what and where, you'll never be able to recover the app from backup without recovering everything from backup. Of course, if you reinstalled to fix problems, you want to import as little as possible from your backup, so you'd be strongly advised to reinstall the apps from scratch anyway.

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