Whoa gnarly dude! That is totally way faster! Here's the details on what I am doing in case anyone spots something totally stupid on my part ...

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

my %seen;

my @logfiles = glob ( "*access_log" );
foreach my $logfile (@logfiles) {
        open ( MYLOG, ">>progress_safe" );
        print MYLOG "Doing $logfile\n";
        close ( MYLOG );
        process_file( $logfile );
}

sub process_file {
        my $fn = shift;
        open ( FH, "<$fn" );
        while (<FH>) {
                chomp;
                s/\W/_/g;
                my $new_empty_file = substr( $_, 0, 200 );
                my $target = "$new_empty_file";
                if ( $seen{$target} && ($fn ne $seen{$target}) ) {
                        $seen{$target} = "$seen{$target} and $fn both 
+have :$target\n";
                        open ( DUP, ">>dups_found_safe" );
                        print DUP "$seen{$target}";
                        close DUP;
                } else {
                        $seen{$target} = "$fn";
                }
        }
}
[download]

... thanks Joost and Monks!