Just diff by character. Something like this ?

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1207184

use strict;
use warnings;
use Algorithm::Diff qw(traverse_sequences);
use Term::ANSIColor;

my $file1 = <<'END';
#!/usr/bin/perl

use Algorithm::Diff qw(traverse_sequences);
use Term::ANSIColor;
use strict;
use warnings;

# line in both files

# line only in file1

my @from = split //, shift // 'this is the left string';
my @to = split //, shift // 'this is the right string';

traverse_sequences( \@from, \@to,
  {
  MATCH     => sub {print $from[shift()]},
  DISCARD_A => sub {print color('red'), $from[shift()], color 'reset'}
+,
  DISCARD_B => sub {print color('green'), $to[pop()], color 'reset'},
  } );
print "\n";
END

my $file2 = <<'END';
#!/usr/bin/perl

use Algorithm::Diff qw(traverse_sequences);
use Term::ANSIColor;
use warnings;
use strict;

# line in both files

my @from = split //, shift // 'this is the source string';
my @to = split //, shift // 'this is the target string';

# line only in file2

traverse_sequences( \@from, \@to,
  {
  MATCH     => sub {print $from[shift()]},
  DISCARD_A => sub {print color('darkred'), $from[shift()], color 'res
+et'},
  DISCARD_B => sub {print color('cyan'), $to[pop()], color 'reset'},
  } );
print "\n";
END

my @from = split //, $file1;
my @to = split //, $file2;

traverse_sequences( \@from, \@to,
  {
  MATCH     => sub {print $from[shift()]},
  DISCARD_A => sub {print color('red'), $from[shift()], color 'reset'}
+,
  DISCARD_B => sub {print color('green'), $to[pop()], color 'reset'},
  } );
print "\n";
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Output not shown because it contains ANSI color sequences. Run in a terminal (like linux console or xterm) that can handle them.