my @stack;
while ($file =~ m{\G(.*)<\?(.*)\?>}gms) {
  my $pre = $1;
  my $pi = $1;
  my @args = split(' ', $pi); # hopefully this always works
  my $pi_cmd = uc($args[0]);
  if ($pi_cmd eq 'CLG.MDFO') {
    # parse next element tag
    if ($file =~ m{\G\s*<\s*([^>\s]*?)(.*?)>}gms) {
      my $element = $1;
      push(@stack, $element);
    }
  } elsif ($pi_cmd eq 'CLG.MDFC') {
    # parse previous element tag
    if ($pre =~ m{<\s*([^>\s]*?)([^>]*)>\s*\z}ms) {
      my $element = $1;
      unless ($element eq pop(@stack)) {
        ...emit mismatch warning ... 
      }
    }
  }
}
if (@stack) {
  ...emit unterminated CLG.MDFO warning...
}

##</code><code>##

</ARTICLE>
<?no_smark?>
<?CLG.MDFC ID="C001001M00 ...

##</code><code>##

my $pre_element;
my @stack;
while ($file =~ m{...regex for a pi...}) {
  my $pre = $1;
  ...
  if ($pi_cmd eq 'CLG.MDFO') {
    ...same as above...
  } else {
    if ($pre =~ m{...regex for element tag...\z}) {
      $pre_element = $1;
    }
    if ($pi_cmd = 'CLG.MDFC') {
      unless ($pre_element = pop(@stack)) {
        ...
      }
    }
  }
}