[dnanian]

If you're comfortable with the shell, let's try this, then. Shut your Mac down and hold down Shift. Power on, and keep Shift down until you get to the desktop. That'll prevent Spotlight from running at all.

Then, in the shell, delete the ".Spotlight_V100" folder at the top of the backup drive.

Restart your Mac, and add the drive into privacy (make sure you're running as an admin).

As far as the double-apps go, LaunchServices will seek-and-find applications on drives that are mounted. Often, as long as the files have been copied and haven't been updated, and use use Smart Update, it won't find them again (unless you view the folder in Finder). So -- if you do it once, you might not have to again for a while.

To help protect against this behavior, you can eject your destination. Note that SD! will automatically mount/copy/eject when a scheduled backup is done.

Finally, to see what might be keeping a drive from ejecting, use "lsof" in the shell, and search for the volume name with grep.