I think you're taking the wrong approach. You might try something like:

use File::Find;
my $oldroot = shift;
my $newroot = shift;
find(\&wanted, $oldroot);

sub wanted {
    # Chop off $oldroot prefix, glom on $newroot prefix
    print $newroot, substr($File::Find::name,length($oldroot), "\n";
}
[download]

Note: Untested code, you'll likely need to fix it.