A few things to keep in mind while you learn Perl:

• Always use strictures (use strict; use warnings).
• Use the three parameter version of open.
• Use consistent indentation.
• Don't use C style for loops unless you really really must.

Consider the following "cleaned up" version of your added code:

my @info = sort keys %{$freqs{all}};
my %countop;

for my $story1 (@info) {
    next if $story1 eq 'total';
    
    for my $story2 (@info) {
        next if $story2 eq 'total';
        
        for my $word (sort keys %freqs) {
            next unless $freqs{$word}{$story1};
            next unless $freqs{$word}{$story2};

            $countop{$story1}{$story2}++;
        }
    }
}

for my $m (sort keys %countop) {
    for my $n (sort keys %{$countop{$m}}) {
        printf OUT1 "$m, $n, $countop{$m}{$n}\n";
    }
}
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