It may help if you clarify what it is that you actually want. Is it the summary data only, the current table with summary data, or something else you haven't mentioned.

It's also appreciated if you indicate up front that you are seeking help with homework ("however i need to hand in perl code"), although CB comments indicate that this may not be exactly homework ("need to do this for a thesis ... no perl, perl is just a way"). Any any case a little background on what you are trying to achieve can save a lot of time all round.

Update: The following may be what you are after:

use strict;
use warnings;

my %freqs;
my $story; # Current story name

while (<DATA>) {
    if (/^\[(.*)\]\s*$/) {
        $story = ucfirst $1; # Force title caps
        die "Duplicate story title: $story" if exists $freqs{$story};
        next;
    }
    
    next unless defined $story; # wait until we have a story title

    for my $word (/\w+/g) {
        # Current story counts
        $word = ucfirst $word;
        $freqs{$word}{$story}++;
        $freqs{all}{$story}++;
        
        # Total counts
        $freqs{$word}{total}++;
        $freqs{all}{total}++;
    }
}

# Print title line
print "\t", (join "\t", sort keys %{$freqs{all}}), "\n";

# Print table
for my $word (sort keys %freqs) {
    $freqs{$word}{$_} ||= 0 for keys %{$freqs{all}};
    printf "$word\t";
    print join "\t", join "\t", map $freqs{$word}{$_}, sort keys %{$fr
+eqs{$word}};
    print "\n";
}

__DATA__
[para one]
Hello everyone! Just to make everything clear. I need this for a proje
+ct were I
am being graded. However, the project is not about Perl. It is about d
+oing
statistics with unstructured data, ie text. I can do this on excel man
+ually, but
I think it would be nice to have a code that will generalyze my analys
+is and
algorithm to any collection of texts. The final goal is to create a pr
+ocess to
classify text and information, with no human interaction. That is what
+ I being
graded on and I do not need help on that. Just perl... counting words 
+in text
and stuff like that. Here is my question Given this code

[para two]
this code takes a multiple pieces of text and creates a table with the
+ words
that appear on each story as rows and story titles as columns. Then ea
+ch "cell"
counts the number of times each word appears on each story So for exam
+ple Story
One: Perl is great Story Two: Perl is free perl Story three: Will I le
+arn perl?
will return:
[download]

Prints:

    Para one    Para two    total
A    3    2    5
About    2    0    2
Algorithm    1    0    1
Am    1    0    1
Analysis    1    0    1
And    4    2    6
Any    1    0    1
Appear    0    1    1
Appears    0    1    1
As    0    2    2
Be    1    0    1
Being    2    0    2
But    1    0    1
Can    1    0    1
Cell    0    1    1
Classify    1    0    1
Clear    1    0    1
Code    2    1    3
Collection    1    0    1
Columns    0    1    1
Counting    1    0    1
Counts    0    1    1
Create    1    0    1
Creates    0    1    1
Data    1    0    1
Do    2    0    2
Doing    1    0    1
Each    0    4    4
Everyone    1    0    1
Everything    1    0    1
Example    0    1    1
Excel    1    0    1
Final    1    0    1
For    1    1    2
Free    0    1    1
Generalyze    1    0    1
Given    1    0    1
Goal    1    0    1
Graded    2    0    2
Great    0    1    1
Have    1    0    1
Hello    1    0    1
Help    1    0    1
Here    1    0    1
However    1    0    1
Human    1    0    1
I    6    1    7
Ie    1    0    1
In    1    0    1
Information    1    0    1
Interaction    1    0    1
Is    5    2    7
It    2    0    2
Just    2    0    2
Learn    0    1    1
Like    1    0    1
Make    1    0    1
Manually    1    0    1
Multiple    0    1    1
My    2    0    2
Need    2    0    2
Nice    1    0    1
No    1    0    1
Not    2    0    2
Number    0    1    1
Of    1    2    3
On    3    2    5
One    0    1    1
Perl    2    4    6
Pieces    0    1    1
Process    1    0    1
Project    2    0    2
Question    1    0    1
Return    0    1    1
Rows    0    1    1
So    0    1    1
Statistics    1    0    1
Story    0    6    6
Stuff    1    0    1
Table    0    1    1
Takes    0    1    1
Text    3    1    4
Texts    1    0    1
That    4    1    5
The    2    2    4
Then    0    1    1
Think    1    0    1
This    3    1    4
Three    0    1    1
Times    0    1    1
Titles    0    1    1
To    5    0    5
Two    0    1    1
Unstructured    1    0    1
Were    1    0    1
What    1    0    1
Will    1    2    3
With    2    1    3
Word    0    1    1
Words    1    1    2
Would    1    0    1
all    114    63    177
[download]