Okay maybe this is what you want:

open MISS, 'missing.txt' or die "Cant open missing: $!\n";
my %missing = map {(lc($_),$_)} <MISS>;
close MISS;

opendir DIR, '.' or die "Can't open pwd: $!\n";
while (defined($_=readdir(DIR))) {
  # convert filename to lowercase and see if it is in list
  if (exists $missing{lc($_)} ) {
    symlink($_, $missing{lc($_)});
    delete $missing{lc($_)};
  }
}
closedir DIR;

print "Still not found:\n\n" . join("\n", keys %missing) . "\n";
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Updated: So the hash keys and input filenames are now compared in lowercase, but the symlinks are done with both original cases.
If you need to rename the files recursivly then be sure to use File::Find.