Hey, Ed. (Hopefully, it's Ed -- slap me if not.)
Hey, it's not paranoia if the OS is out to get you, right?
OK, so -- "Backup - all files" doesn't share anything with the main volume. So, you can make that clone then *detach* the external and put it aside so Tiger doesn't touch it (think "Spotlight"). Then, go ahead and upgrade to Tiger (no need to Clean Install right out of the gate), and you should be good to go.
If you want to clean install, you'll have to attach the Panther copy when it asks to Migrate your settings. But, that lets Tiger touch the drive, so be aware!
Hope that helps.