The way I understand your logic, the following code should work even for the cases like

Pass Fail New
p1   
-     p1 
p1
p1
p2
-     p3
-     -    p4

Your Unique will be 3 in this case. (for p1,p2,p4).

I have assumed that for the output table, your primary key consists of agency, url and module as figured out from the results.

use strict;
use warnings;
use Data::Dumper;
my $hash;
while(<DATA>){
    chomp;
    my @fields = split /\s+/;
    my ($agency,$url,$mod) = @fields[2,3,6];
    my ($user,$state) = @fields[1,5];
    my $item = $hash->{$agency}{$url}{$mod};
    if($state eq 'pass'){
               $hash->{$agency}{$url}{$mod}{pass} += 1;
    }elsif($state eq 'fail'){
               $hash->{$agency}{$url}{$mod}{fail} += 1;
    }
    elsif($state =~ /new_/){
               $hash->{$agency}{$url}{$mod}{new} += 1;
    }
    $hash->{$agency}{$url}{$mod}{users}{$user} += 1 if $state ne 'fail
+';
}
print join "\t" => qw(Agency URL Pass Fail New Unique Module),"\n";
foreach my $agency (keys %{$hash}){
    foreach my $url (keys %{$hash->{$agency}}){
    foreach my $mod (keys %{$hash->{$agency}{$url}}){
        my $item = $hash->{$agency}{$url}{$mod};
        my $pass = $item->{pass} || 0;
        my $fail =$item->{fail} || 0;
        my $new = $item->{new} || 0;
        my $unique =scalar keys %{$item->{users}};
        print join "\t" => ($agency,$url,$pass,$fail,$new,$unique,$mod
+),"\n";
    }
    }

}
    
__DATA__
05/Jun/2003:00:01:23 user1 agency1 url1 garbage pass mod1 more_garbage
05/Jun/2003:00:03:17 user2 null url1 garbage fail mod1 more_garbage
05/Jun/2003:00:03:42 user1 agency1 url1 garbage pass mod1 more_garbage
05/Jun/2003:00:05:03 user6 agnecy2 url1 garbage pass mod1 more_garbage
05/Jun/2003:00:08:34 user3 agnecy2 url1 garbage pass mod1 more_garbage
05/Jun/2003:00:11:59 user4 agency2 url2 garbage fail mod1 more_garbage
05/Jun/2003:00:14:30 user5 agnecy2 url1 garbage new_a mod1 more_garbag
+e
05/Jun/2003:00:15:02 user1 agency1 url1 garbage pass mod1 more_garbage
05/Jun/2003:00:16:56 user7 agency2 url2 garbage pass mod2 more_garbage
05/Jun/2003:00:17:31 user1 agency1 url1 garbage fail mod1 more_garbage
05/Jun/2003:00:17:31 user1 agency1 url1 garbage pass mod2 more_garbage
[download]

Agency	URL	Pass	Fail	New	Unique	Module	
null	url1	0	1	0	0	mod1	
agency1	url1	3	1	0	1	mod1	
agency1	url1	1	0	0	1	mod2	
agency2	url2	0	1	0	0	mod1	
agency2	url2	1	0	0	1	mod2	
agnecy2	url1	2	0	1	3	mod1

artist