Use the code below to say matched element count also, this will tell you the possible matches not only twice.

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

my %hash_count;
my @array =  ( "54321", "54312" ,    "5999" ,    "54352" ,    "12345" 
+   );

  my @original =    ( "12345" ,    "54321" ,    "12355", "54321"    );

    foreach my $string(@array)
    {
        foreach my $string2(@original)
        {
            if ($string eq $string2) {
                $hash_count{$string}++;
            }
            else
            {
                unless (exists $hash_count{$string})
                {
                    $hash_count{$string} = 0;
                }
            }

        }
    }

print Dumper \%hash_count;

foreach (keys %hash_count)
{        
    unless ($hash_count{$_}) {
            print "$_ Not found\n";
    }   
    else
    {   
            print "$_ found $hash_count{$_} times\n" ;
    }
}
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Track counts instead of assign 1 to hash:

use strict   ;
use warnings ;


my @array    = ( "54321", "54312", "5999", "54352", "12345" ) ;
my @original = ( "12345" , "54321" , "12345"       ) ;

my %count ;
map( { $count{ $_ }++ } @original );

print "". ( ( $count{ $_ } ) ? "$_ Found $count{ $_ } times.\n" : "$_ 
+Not Found\n" ) foreach ( @array ) ;
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Output:

54321 Found 1 times.
54312 Not Found
5999 Not Found
54352 Not Found
12345 Found 2 times.
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Thanks a million guys!! Much appreciated! I can use each of these in different areas. Now just for me to go sit rewrite everything in my code to open the files and get arrays of the data. Again, thanks a mill for the help!!

just try this one

#!C:\Perl64\bin -w
use strict;
my @array =
    (
    "54321" ,
    "54312" ,
    "5999" ,
    "54352" ,
    "12345"
    );
my @original =
    (
    "12345" ,
    "54321" ,
    "12355"
    );
my $hash={};
foreach my $val(@original){
    if (grep{$_ == $val} @array){
        $hash->{$val}++;
    }##end if
    else {
        print "$val NOT MATCHED\n";
    }##end else
}##end foreach
foreach (keys(%{$hash})){
    print "$_ matched $hash->{$_} times\n";
}##end foreach
[download]