So here is an example using the flip-flop operator - however I am not certain what the OP is actually looking for:

use strict;
use warnings;
use Data::Dumper;

my @sections;

while (<DATA>) {
    chomp;
    if (/===Comments===/../^[^=]/) {
        if (/===Comments===/) {
            push @sections,[] 
        }
        else {
            push @{$sections[-1]}, $_ if $_
        }
    }
    
}

print Dumper(\@sections);
[download]

Which for the supplied data gives:

$VAR1 = [
          [
            'User comments are added here. A user may write whatever t
+hey may wish.'
          ],
          [
            'Comments are related to the microarray data here.'
          ],
          [
            'Comments related to the pathway information here.'
          ]
        ];
[download]