Here's a solution using an array slice.

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;

use List::Util qw{shuffle};

my $array_elements = 60;    # originally 600
my $random_elements = 3;    # originally 10
my $no_of_arrays = 10;      # originally 1000
my $norm_char = q{-};
my $rand_char = q{X};

my @all_strings = ();

for (1 .. $no_of_arrays) {
    my @tmp_array = ($norm_char) x $array_elements;

    @tmp_array[(shuffle 0 .. $array_elements - 1)[0 .. $random_element
+s - 1]]
        = ($rand_char) x $random_elements;

    push @all_strings => join q{} => @tmp_array;
}

map { say } @all_strings;
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