Regex/pattern matching trouble

<!--start1-->
<link href="sidenavs.css" rel="stylesheet" type="text/css" />
<div id="sidenavs">
<h1>Products</h1>
<ul>
<li><a href="#" class="side1"><!--startside1-->Application Virtualization<!--endside1--></a>
	<div id="subnavs1" style="display: none;">
	<ul>
		<li><a href="#" class="sub1"><!--startsub1-->Activity Recording<!--endsub1--></a>
		<li><a href="#" class="sub2"><!--startsub2-->Rollback<!--endsub2--></a>
		<li><a href="#" class="sub3"><!--startsub3-->Application Migration<!--endsub3--></a>
		<li><a href="#" class="sub4"><!--startsub4-->Workspace Mobility<!--endsub4--></a>
		<li><a href="#" class="sub5"><!--startsub5-->Application Footprint Cleanup<!--endsub5--></a>
	</ul>
	</div>
<li><a href="#" class="side2"><!--startside2-->Asset Management<!--endside2--></a>
<li><a href="#" class="side3"><!--startside3-->Remote Terminal<!--endside3--></a>
<li><a href="#" class="side4"><!--startside4-->What's New<!--endside4--></a>
</ul>
</div>
<!--end1-->

<!--start2-->
<link href="sidenavs.css" rel="stylesheet" type="text/css" />
<div id="sidenavs">
<h1>Technology</h1>
<ul>
<li><a href="#" class="side5"><!--startside5-->Virtualization<!--endside5--></a> 
<li><a href="#" class="side6"><!--startside6-->SaaS<!--endside6--></a>
<li><a href="#" class="side7"><!--startside7-->Deployment<!--endside7--></a>
<li><a href="#" class="side8"><!--startside8-->Reporting<!--endside8--></a>
</ul>
</div>
<!--end2-->

<!--start3-->
<link href="sidenavs.css" rel="stylesheet" type="text/css" />
<div id="sidenavs">
<h1>Resources</h1>
<ul>
<li><a href="#" class="side9"><!--startside9-->Trial Evaluation<!--endside9--></a>
<li><a href="#" class="side10"><!--startside10-->Demo<!--endside10--></a>
<li><a href="#" class="side11"><!--startside11-->ROI Calculator<!--endside11--></a>
<li><a href="#" class="side12"><!--startside12-->Links to external sources (hidden)<!--endside12--></a>
</ul>
</div>
<!--end3-->

<!--start4-->
<link href="sidenavs.css" rel="stylesheet" type="text/css" />
<div id="sidenavs">
<h1>Company</h1>
<ul>
<li><a href="#" class="side13"><!--startside13-->About Us<!--endside13--></a>
<li><a href="#" class="side14"><!--startside14-->Investors<!--endside14--></a>
<li><a href="#" class="side15"><!--startside15-->Office Locations<!--endside15--></a>
</ul>
</div>
<!--end4-->

<!--start5-->
<link href="sidenavs.css" rel="stylesheet" type="text/css" />
<div id="sidenavs">
<h1>Support</h1>
<ul> 
<li><a href="#" class="side16"><!--startside16-->Login<!--endside16--></a>
</ul>
</div>
<!--end5-->

<!--start6-->
<link href="sidenavs.css" rel="stylesheet" type="text/css" />
<div id="sidenavs">
<h1>Partners</h1>
<ul>
<li><a href="#" class="side17"><!--startside17-->MSP<!--endside17--></a>
<li><a href="#" class="side18"><!--startside18-->Become a partner<!--endside18--></a>
<li><a href="#" class="side19"><!--startside19-->Login<!--endside19--></a>
</ul>
</div>
<!--end6-->

<!--start7-->
<link href="sidenavs.css" rel="stylesheet" type="text/css" />
<div id="sidenavs">
<h1>News</h1>
<ul>
<li><a href="#" class="side20"><!--startside20-->Press Releases<!--endside20--></a>
<li><a href="#" class="side21"><!--startside21-->In the News<!--endside21--></a> 
<li><a href="#" class="side22"><!--startside22-->Events<!--endside22--></a>
<li><a href="#" class="side23"><!--startside23-->Media Kit<!--endside23--></a>
</ul>
</div>
<!--end7-->

if ($sideunlink){	
	$holder =~ s/<a href=".*" class="sidenavlit">(<!--startside$sidelit-->.*<!--endside$sidelit-->)<\/a>/$1/;
}

if ($subunlink){	
	$holder =~ s/<a href=".*" class="subnavlit">(<!--startsub$sublit-->.*<!--endsub$sublit-->)<\/a>/$1/;
}

#!/usr/bin/perl -wT
use strict;
use CGI ':standard';

use CGI::Carp qw(fatalsToBrowser);

my $sidegroup = param('sidegroup');		# indciates which sidenav group to show
my $sidelit = param('sidelit');			# indicates which sidenav is to be lit
my $sideunlink = param('sideunlink');	# any non-zero value indicates the lit sidenav should not be linked
my $subgroup = param('subgroup');		# indicates which subnav group to show
my $sublit = param('sublit');			# indicates which subnav is to be lit
my $subunlink = param('subunlink');		# any non-zero value indicates the lit subnav should not be linked

my $holder;								# holds the navs to be printed

### Open nav template and put into $holder
### You must chomp because the upcoming pattern matching breaks on newlines

open(NAVS,"sidenavs.html") || die "Couldn't open file: $!";
	foreach (<NAVS>){ 
		chomp;
		$holder .= $_;
	}
close(NAVS);

### Extract the required group of navs

$holder =~ m/(<!--start$sidegroup-->.*<!--end$sidegroup-->)/g;
$holder = $1;

### Apply styles according to params

if ($sidelit){
	$holder =~ s/class="side$sidelit"/class="sidenavlit"/;
}

if ($subgroup){
	$holder =~ s/<div id="subnavs$subgroup" style="display: none;">/<div id="subnavs">/;
}

if ($sublit){
	$holder =~ s/class="sub$sublit"/class="subnavlit"/;
}

### Remove links if specified by params

if ($sideunlink){	
	$holder =~ s/<a href=".*" class="sidenavlit">(<!--startside$sidelit-->.*<!--endside$sidelit-->)<\/a>/$1/;
}

if ($subunlink){	
	$holder =~ s/<a href=".*" class="subnavlit">(<!--startsub$sublit-->.*<!--endsub$sublit-->)<\/a>/$1/;
}

### Apply styles to non-specific navs (those not specified in params)

$holder =~ s/class="side\d+"/class="sidenav"/g;
$holder =~ s/class="sub\d+"/class="subnav"/g;

### Print the navs

print "Content-type: text/html\n\n";
print $holder;

sidenavs.pl?sidegroup=1&sidelit=1&sideunlink=1&subgroup=1&sublit=3&subunlink=1

<!--start1-->
<link href="sidenavs.css" rel="stylesheet" type="text/css" />
<div id="sidenavs">
  <h1>Products</h1>
  <ul>
    <li>
      <!--startside1-->
      Application Virtualization
      <!--endside1-->
      <div id="subnavs">
        <ul>
          <li>
            <!--startsub3-->
            Application Migration
            <!--endsub3-->
          <li><a href="#" class="subnav">
            <!--startsub4-->
            Workspace Mobility
            <!--endsub4-->
            </a>
          <li><a href="#" class="subnav">
            <!--startsub5-->
            Application Footprint Cleanup
            <!--endsub5-->
            </a>
        </ul>
      </div>
    <li><a href="#" class="sidenav">
      <!--startside2-->
      Asset Management
      <!--endside2-->
      </a>
    <li><a href="#" class="sidenav">
      <!--startside3-->
      Remote Terminal
      <!--endside3-->
      </a>
    <li><a href="#" class="sidenav">
      <!--startside4-->
      What's New
      <!--endside4-->
      </a>
  </ul>
</div>
<!--end1-->

<!--start1-->
<link href="sidenavs.css" rel="stylesheet" type="text/css" />
<div id="sidenavs">
  <h1>Products</h1>
  <ul>
    <li>
      <!--startside1-->
      Application Virtualization
      <!--endside1-->
      <div id="subnavs">
        <ul>
          <li><a href="#" class="subnav">
            <!--startsub1-->
            Activity Recording
            <!--endsub1-->
            </a>
          <li><a href="#" class="subnav">
            <!--startsub2-->
            Rollback
            <!--endsub2-->
            </a>
          <li>
            <!--startsub3-->
            Application Migration
            <!--endsub3-->
          <li><a href="#" class="subnav">
            <!--startsub4-->
            Workspace Mobility
            <!--endsub4-->
            </a>
          <li><a href="#" class="subnav">
            <!--startsub5-->
            Application Footprint Cleanup
            <!--endsub5-->
            </a>
        </ul>
      </div>
    <li><a href="#" class="sidenav">
      <!--startside2-->
      Asset Management
      <!--endside2-->
      </a>
    <li><a href="#" class="sidenav">
      <!--startside3-->
      Remote Terminal
      <!--endside3-->
      </a>
    <li><a href="#" class="sidenav">
      <!--startside4-->
      What's New
      <!--endside4-->
      </a>
  </ul>
</div>
<!--end1-->