Hello jjohhn ,

This might be a little 'quick and dirty' but it does what you want, using a hash :

use strict ; 
use warnings ; 

my @file1 = ( 'A1|dog|', 'A2|cat|','A3|bird|' ) ; 
my @file2 = ( 'A1|Fido|','A2|Fluffy|','A3|Tweety|') ; 
my %rez ;

foreach  my $it (@file1) { 
my @input = split /\|/ , $it ;
$rez{$input[0]} = join "|" ,"", @input[1,] ;
}

foreach  my $it (@file2) { 
my @input = split /\|/ , $it ;
$rez{$input[0]} .= join "|" ,"", @input[1,] ;
}

print $_, $rez{$_}, "\n" foreach ( sort keys %rez )   ;
[download]

Hope this helps :)
zlr_