There are some very clever ways to do this, but simple is probably easiest: why not just include the string ===Comments=== in your regular expression twice?

if(Dumper($page) =~ /===Comments===(.*?)=Microarray Data=/s.*?===Comme
+nts===(.*)) {  
            $lit_comments = $1; 
            $second_comments = $2;
        }
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See perlretut for some reference material.