OK, you may need to adjust the definition of $total as indicated somewhere; otherwise following program works as i understood your problem...

#! /usr/local/bin/perl -w

use strict ;

my $stopfile = 'stopwords';
my %stoplist;

#  fill stop word list assuming each word is on one line
open STOP, "<$stopfile"
  or die "cannot open $stopfile: $!\n";

while ( defined (my $stop = <STOP>) )
{
  chomp $stop;
  $stoplist{$stop} = 1;
}

close STOP or die "cannot close $stopfile: $!\n";

#  FIRST file contains the words to compare against,
#  get the target word list
#
my @target = @{ filter( \%stoplist , [ shift @ARGV ] ) };

#  rest of the files contain words which we want
#  to compare against the target list
#
my @words = @{ filter( \%stoplist , \@ARGV ) };

#  adjust as desired as i fail to see what is @D1 (in OP) and
#  why $total needs to be the twice the size of @D1
#
#  BELOW IS MY NOTION OF $total
#
my $total = scalar @target + scalar @words;

my $similarity =
  2 * ( scalar @{ intersect( \@target , \@words ) }
        / $total
      );

#  display similarity upto 4 decimal places
printf "\nsimilarity is: %0.4g\n\n", $similarity;


#  find intersection of two arrays: 1st contains all the interesting v
+alues,
#  2d both interesting & uninteresting
sub intersect
{
  my ($ref , $misc) = @_;

  my %intersection;

  foreach my $misc ( @{$misc} )
  {
    foreach my $ref ( @{$ref} )
    {
      next if $misc ne $ref;
      $intersection{$ref} = 1;
    }
  }

  return [ keys %intersection ];
}


#  given a stop word hash & file name array (consisting of input word 
+list),
#  return the word list that are not stop words
sub filter
{
  my ($stop , $files) = @_;

  my %filtered;

  foreach my $file ( @{$files} )
  {
    open FH , "<$file"
      or die "cannot open $file to read: $!\n";

    while ( defined (my $line = <FH>) )
    {
        foreach my $word (@{ line2words( $line ) })
        {
          next if $stop->{$word};
          $filtered{$word} = 1;
        }
    }

    close FH or die "cannot close $file: $!\n";
  }

  return [ keys %filtered ];
}

#  return words, lower cased, from a given line
sub line2words
{
  my $line = $_[0];

  return
    [ map { lc $_ }
        grep { $_ ne '' }
          split /\W+/ , $line
    ];
}
[download]

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Update: Add missing die if cannot close STOP.

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