I guess you want to do something like this:

# untested!
open my $fh1, ...
open my $fh2, ...

my %pairs;

while (1) {
  my $l1 = <$fh1>;
  my $l2 = <$fh2>;
  last unless (defined $l1 and defined $l2);

  my @l1 = $l1 =~ /\w+/g;
  my @l2 = $l2 =~ /\w+/g;

  for my $w1 (@l1) {
    for my $w2 (@l2) {
      $pairs{"$w1-$w2"}++;
    }
  }
}

my @sorted = sort { $pairs{$b} <=> $pairs{$a} } keys %pairs;
for my $k (@sorted) {
  say "$pairs{$k} ==> $k"
}
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