Assuming there will always be a match for those two flags, and that there are only one of each of those flags in each page:

($text) = $text =~ /<!-- END MAIN HEADER CODE -->(.*?)<!-- END BOTTOM 
+CHAPTER\/SECTION NAV CODE -->/s;
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Or, as someone pointed out on CB, you can also use index / rindex / substr:

my $start = '<!-- END MAIN HEADER CODE -->';
my $end = '<!-- END BOTTOM CHAPTER/SECTION NAV CODE -->';

my $index = index($text, $start) + length($start);
$text = substr($text, $index, rindex($text, $end) - $index);
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