Just for fun...

use strict;
use warnings;
use autodie;

use Getopt::Long;
use File::Slurp qw( read_file write_file );
use List::MoreUtils 'pairwise';

use constant {
  EMPTY => q{},
  FILE1 => 'e:/File1.txt',
  FILE2 => 'e:/File2.txt'
};

my $LIVE = EMPTY;
GetOptions('live' => \$LIVE);


write_file
  $LIVE ? FILE2 : \*STDOUT,
  pairwise {
    join( ',', map{$_//EMPTY} $a,$b ) . "\n";
  } @{slurp(FILE1)}, @{slurp(FILE2)};


sub slurp { read_file shift, array_ref=> 1, chomp => 1 }
[download]

By default this will dump its output to STDOUT. Once you're certain it will do what you want, run it with the --live flag, and it will overwrite FILE2, which seems to be what you want. I'd probably use copies of the original files until I'm certain.

Updated: Handle command-line option via Getopt::Long rather than @ARGV.