1. For every elements in array

 2. Assign elem[0] of array in key1,key2,key3 etc to an empty array 
    (we call it: $AoA[0])
    So it'll be as many as 4 arrays (= size of array in hash)
    e.g. $AoA[0] ..$AoA[3] filled up with elem[0] of all hashes
         $AoA[0][0]="A",$AoA[1][0] ="B", $AoA[2][0]="C",$AoA[3][0]="D"

    Or if you will at this point we have @AoA = ([A],[B],[C],[D])

    Every element of arrays in first key *becomes* first element 
    of new array in @AoA

 3. Check if the elements of next array are equal
    e.g Check: elem[0]-key1 = elem[0]-key2

 4. If they are equal, store elem[0]-key2 in $AoA[0], 
    then go to next hash (elem[0]-key3)..etc

 5. If they are not equal, check if elem[0]-key1 = elem[1]-key2 ..etc 
    until elem[last]-key2 (exhaust all element of array in key2)
    If they are >1 matches, take only the *first* matching one.
    If after exhausting it, still cannot find, 
    assign '-' (dash) to $AoA[0] etc.

 6. While checking, check elem[0]-key1 ..elem[last]-key1 
    with elements of next array of key2-key4, 
    verify if elem[0]-key2 has been *used* for previous match,
    if yes then check elem[0]-key1 = elem[1]-key2, 
                                   = elem[2]-key2  ...
                                   = elem[last]-key2, 
    otherwise match it (assign elem[0]-key1 = elem[0]-key2 ).

 7. Finally we have an AoA with $AoA[1] ..$AoA[4] filled up 
    (see answers snippet below)
[download]

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my %hoa1 = (
             'key1' => ["A","B","C","D"],
             'key2' => ["A","C","D","B"],
             'key3' => ["C","A","D","H"],
             'key4' => ["A","B","I","C"],
         );

my %hoa2 = (
             'key1' => ["A","D"],
             'key2' => ["A","B"],
             'key3' => ["C","H"],
         );

my @answ = align_array(%hoa1);
print Dumper \@answ;

sub align_array
{
    my %hoa = @_;
    my @AoA;
    my @keys = sort keys %hoa;

    foreach my $id ( -1 .. $#keys-1  )
    {

       for  ( 0 .. $#{$hoa{$keys[$id]}}  )
       {
           #Here I get point No.2 done
           $AoA[$_][0] = $hoa{$keys[0]}[$_];

           # I'm totally stuck here, in attempt to do point No.3 to 7
           # How can I evaluate elements of array of varying size
           # dynamically?
          
           if ( $AoA[$_][0] =  $hoa{$keys[$id+1]}[$_] )
           {
               $AoA[$_][$_+2] = $hoa{$keys[$id+1]}[$_];
           }
           elsif ( $AoA[$_][0] =  $hoa{$keys[$id+3]}[$_] )
           {
            $AoA[$_][$_+2] = $hoa{$keys[$id+3]}[$_];
           }
           else
           {
               $AoA[$_+1][$_+2] = "-";
           }

      }

    }                               # -----  end foreach  -----

        return @AoA ;
}
[download]

# For @answ_hoa1, note that 2nd elem of 4th array is "-" and not "D"
# because elem[last] in 2nd array ("B") has been *used* before

my @answ_hoa1 = (
                  ["A","A","A","A"],
                  ["B","B","-","B"],
                  ["C","-","-","C"],
                  ["D","-","D","-"],
               );

my @answ_hoa2 = (
                 ["A","A","-"],
                 ["D","-","-"],
               );
[download]