i can open a file handle but I dont know how to print the entire table to a file

Let's assume you opened filehandle REPORT. The following code from Grandfather

    for my $word (sort keys %freqs) {
        $freqs{$word}{$_} ||= 0 for keys %{$freqs{all}};
        printf "$word\t";
        print join "\t", join "\t", map $freqs{$word}{$_}, sort keys %
+{$freqs{$word}};
        print "\n";
    }
[download]

could be changed to:

    for my $word (sort keys %freqs) {
        $freqs{$word}{$_} ||= 0 for keys %{$freqs{all}};
        printf REPORT "$word\t";
        print REPORT join "\t", join "\t", map $freqs{$word}{$_}, sort
+ keys %{$freqs{$word}};
        print REPORT "\n";
    }
[download]

The next thing, can I modify this to count the shared words between stories, too?

Certainly. Will you be reading several stories from the same DATA block? Then you don't need to change a thing.

Will you change the program to read from several different input files? How do you want to give those filenames to your program?