talexb is right - you really should be using HTML::Parser for the majority of this thing - a quicky example :

#!/usr/bin/perl -w

use strict;
use HTML::Parser;

my $tagged_string = "<string>text<other tag>more text...\nstring</stri
+ng>another string<string tag>";

my $replace = 'string';

my $parser = HTML::Parser->new(api_version => 3,
                               default_h => [sub {print shift}, 'text'
+],
                               text_h    => [\&text, 'dtext']);

$parser->parse($tagged_string);

sub text
{
  my ( $text ) = @_;

  $text =~ s%\b($replace)\b%<b>$1</b>%sg;
  print $text;
}
[download]

/J\