I have comments in the file and want to grab the stuff between them.

I would consider using HTML::TokeParser. I use the following.

#!/bin/perl5

use strict;
use warnings;
use HTML::TokeParser;

my $file = 'index.html';
my $tp = HTML::TokeParser->new($file)
  or die "Couldn't parse $file: $!";

my ($start, $html);
while (my $tag = $tp->get_token) {

  if ( 
    $tag->[0] eq 'C' and 
    $tag->[1] eq '<!-- article start -->'
  )
  { 
   $start++;
   next;
  }

  next unless $start;

  if (
    $tag->[0] eq 'C' and
    $tag->[1] eq '<!-- article end -->'
  )
  {
    last;
  }

  $html .= $tag->[4] if $tag->[0] eq 'S';
  $html .= $tag->[1] if $tag->[0] eq 'T' or $tag->[0] eq 'C';
  $html .= $tag->[2] if $tag->[0] eq 'E';

}

print "$html\n";

# ["S",  $tag, $attr, $attrseq, $text]
# ["E",  $tag, $text]
# ["T",  $text, $is_data]
# ["C",  $text]
# ["D",  $text]
# ["PI", $token0, $text]
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