The following does what you want. Note that I've excluded all 1 and 2-letter words, plus and and the. You may wish to add to the exclusion list. Also note that I have not provided for the situation where a paragraph word count goes over 999 for a 3-letter word. I didn't feel this was necessary.

use strict;
use warnings;

my (%count, @pcount, @words, @values, $format, $i);

my @remove = qw/and the/; # Words to exclude
my $width = 10;           # Number of words to display

$/ = '-100';              # Line delimiter
while (<DATA>) {
    my %pcount;
    $_ = lc $_;
    while (m/[a-z]+('[a-z]+)?/g) {
        next if length($&) < 3;
        $pcount{$&}++; $count{$&}++;
    }
    push @pcount, \%pcount;
}

for (@remove) { delete $count{$_} if exists $count{$_}; }
@words = sort {$count{$b} <=> $count{$a} || $a cmp $b} keys %count;
$#words = $width - 1 if $#words > $width - 1;

$format = '%' . length($#pcount+1) . 's';
$format .= '%' . (length($_) + 2) . 's' for @words;

print ' 'x10, sprintf($format, '', @words), "\n";
for ($i = 0; $i <= $#pcount; $i++) {
    my @values = $i + 1;
    push @values, $pcount[$i]{$_} for @words;
    no warnings;
    print 'paragraph ', sprintf($format, @values), "\n";
}

push @values, $count{$_} for @words;
print "\n", ' 'x10, sprintf($format, '', @words), "\n";
print ' 'x10, sprintf($format, '', @values), "\n";


__DATA__
So it was into a neighborhood bursting with rumors and resentment that
+ Gopi, the ten year old cousin who had been brought down from the vil
+lage to be the household help, stepped out to do his daily chores. Hi
+s responsibilities included:-100
1. Carrying the copper tray for the old lady and trotting behind her a
+t the proper pace when she went out to do her morning prayers at five
+ am in the morning.-100
2. Bringing the wood, the coal, and the kindling so that the daughter-
+in-law could light the fire.-100
3. Bringing water from the well to the fifth floor, where the kitchen 
+was located.-100
4. Cutting the vegetables, cleaning the rice, soaking the lentils, she
+lling the peas and any other sundry time-consuming tasks that arose i
+n a kitchen with a mortar and pestle and precious little else.-100
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Output:

             that  bringing  from  her  his  kitchen  morning  old
paragraph 1     1               1         2                      1
paragraph 2                          2                      2    1
paragraph 3     1         1                                       
paragraph 4               1     1                  1              
paragraph 5     1                                  1              

             that  bringing  from  her  his  kitchen  morning  old
                3         2     2    2    2        2        2    2
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