As well, as you've posted on this issue before, it's generally considered good form to keep it in a thread or at least cite your previous postings on the issue (I'm guessing Search for Second Occurence of Substing and get containing text and Searching string for paragraph..).

For your actual question, your specification leaves something to be desired. I will read it as "Extract all text following '===Comments===' until the next '=' or end of file and then extract all text following '=Aditional Notes=' until the next '=' or end of file". Note the misspelling of Aditional<sic>. The following will take your posted material and capture the strings in question into arrays. If this does not work for your actual text, post that case so we can have accurate input for test cases.

#!/usr/bin/perl
use strict;
use warnings;

my $text = do {
    local $/; #slurp
    <DATA>;
};

my @comments = $text =~ /(?<====Comments===).*?(?==|$)/gs;
my @additional = $text =~ /(?<==Aditional Notes=).*?(?==|$)/gs;
1;
__DATA__
===Comments===

This webpage contains information bla bla bla

=Section 2=

Some more text here.

===Comments===

Some other comments here.

=Another section=

=Aditional Notes=

More notes here.
[download]

What I can't seem to do now is extract the next block of text below the second comments box between "===Comments===" and "=Another Section=", as the start tag is already found earlier in the article.

Second, I'm not sure whether I spot what your problem is here. Could you elaborate?

As a secondary point. I also need to extract all the text after the "=Aditional Notes=" section. The problem is I do not know what the end tag for this will be, as it will be the last word used here (i.e. the last character in the webpage).

Of course, if you just want to match every thing after "=Aditional Notes=", then just use /=Aditional Notes=(?s:.*)/.

m/[=]+Additional Notes[=]+.*?\n(.*)/s; #this (.*) will get all 
                                       #to end of the $page
                                       #see below, ending [=]+ and /g 
+is not
                                       #needed for this job
[download]

#!/usr/bin/perl -w
use strict;

open (IN , '<', "awebpage.txt") or die;

my @page = <IN>;           #this is like a "slurp" into a scalar
my $page = join('',@page); #with undef record seperator

my @comments = $page =~ m/[=]+Comments[=]+.*?\n(.*?)[=]+/gs;

my $count =1;
foreach (@comments)
{
   print "COMMENT #$count is:\n$_";
   $count++;
}

=file awebpage.txt is:
A webpage.

===Comments===
This webpage contains information bla bla bla

=Section 2=
Some more text here.
whatever
===Comments===
Some other comments here.
=Another section=
=Aditional Notes=
=Comments=
some more comments and notes here
=Notes=
More notes here.
=cut

=****prints:****
COMMENT #1 is:
This webpage contains information bla bla bla

COMMENT #2 is:
Some other comments here.
COMMENT #3 is:
some more comments and notes here
=cut
[download]

Thanks. That works perfectly. Glad to have put this problem to bed!

I'm also more than a bit suspicious of your data: Is the webpage from which you have "taken" the data a wiki or somesuch?

Or, assuming your data is accurately represented above, using...

might work for multiple comment sections. Sorry, I hate to post untested code, but this is, due to press of time

As to your problem re the end of the page: the last word the server knows about is </html> so the last character will be >, even though that will leave your with some markup tags to remove (possibly "</p></body></html").