To do this, I need to reconcile the discrepancies between the lists and come up with an array of arrays holding the indexes.

Have a look at List::Compare. Following code does build a hash of arrays holding the indexes (you may need to replace the ' ' string (being used for undef values) with undef; I used it in favor of undef, because undef would garble the output). Basically, it should work for an infinite amount of sets.

#!/usr/bin/perl

use strict;
use warnings;

use List::Compare;

my (%have, 
    @seen, 
    %is_unique);

my @sets = (
  [qw( a c f g e h i )],      # X
  [qw( a b c d e f g h i )],  # Y
  [qw( a c d e f g h i )],    # Z
);

my $lcm = List::Compare->new(@sets);

foreach my $set (@sets) {
    my %seen = map { $_ => 1 } @$set;
    push @seen, \%seen;
}

foreach ($lcm->get_intersection) { 
    $have{$_} = [ 0..$#sets ];
}

my %index = map { $_ => undef } 0..$#sets;

foreach my $i (0..$#sets) {
    foreach my $elem ($lcm->get_unique($i)) {
        my @list;    
        foreach (keys %index) { $list[$_] = $index{$_} }
        $list[$i] = $i;
        $have{$elem} = [ @list ];
        $is_unique{$elem}++;
    }
}

foreach my $elem ($lcm->get_nonintersection) {
    next if $is_unique{$elem};
    my @list;
    foreach (keys %index) { $list[$_] = $index{$_} }
    foreach my $i (0..$#sets) { $list[$i] = $i if $seen[$i]{$elem} }
    $have{$elem} = [ @list ];
}    

foreach (sort keys %have) {
    foreach my $i (0..@{$have{$_}}) {
        print defined $have{$_}->[$i] ? "$_ " : '  ';
    }
    print "\n";
}

__OUTPUT__

a a a
  b
c c c
  d d
e e e
f f f
g g g
h h h
i i i
[download]

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