Sounds like a perfect job for XML::Twig.

use strict;
use warnings;

use XML::Twig qw( );


my $fqn_dat = 'mlr.dat';
my $fqn_in  = 'mlr_648.xml';
my $fqn_out = 'fixed_mlr_648.xml';



my %translations;
{
   open(my $fh, '<', $fqn_dat)
      or die("Can't open \"$fqn_dat\": $!\n");

   while (<$fh>) {
      /^(.*?)\t(.*)/ or next;
      $translations{$1} = $2;
   }
}


open(my $fh_in, '<', $fqn_in)
   or die("Can't open input file \"$fqn_in\": $!\n");

open(my $fh_out, '>', $fqn_out)
   or die("Can't create output file \"$fqn_out\": $!\n");

my $twig = XML::Twig->new(   
    twig_handlers => {
       'reference/title[@type="journal"]' => sub {
          my ($twig, $elt) = @_;
          my $text = $elt->text();
          if ( exists( $translations{$text} ) ) {
             $elt->set_text( $translations{$text} );
          } else {
             warn("No translation found for \"$text\"\n");
          }
       },

       'reference' => sub {
          my ($twig, $elt) = @_;
          # Keep at most one <reference> in memory.
          $twig->flush($fh_out);
       },
    }
);

$twig->parse($fh_in);
$twig->flush($fh_out);
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