#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

my @array1 = ("A","A","A","B","C");
my @array2 =  ("a","b","c","d","e");

my %seen;
my @tmp;

for my $i ( 0.. $#array1 ){
    push @tmp, $array1[$i] unless exists $seen{ $array1[$i] };
    push @{ $seen{ $array1[$i] } }, $i;
}

@array1 = @tmp;
undef @tmp;

for my $j ( 0..$#array1 ){
    my $elem = $array1[$j];
    $tmp[$j] = join '', @array2[ @{ $seen{$elem} } ];
}

@array2 = @tmp;

print Dumper \@array1, \@array2;