I don't understand why you keep adding new stuff to your question. Why not at once? Anyway, you don't have to treat the 'QA' and 'DEV' differently, as it contains COM code just like JIRA:

        # save all stored data if we see dashes line
        my $program  = $hash->{Program} || '';
        my $com_code = $hash->{JIRA}    || $hash->{QA} || $hash->{DEV}
+ || '';
        if ( $program && $com_code )
        {
            push @{ $data->{ $program }{ $com_code }}, $hash;
            $hash = {};
        }
[download]

If you used the Dumper( $data ), commented out somewhere in the middle of the code, then you would have seen how the data is set. Based on that, you can change the code (after Dumper statement) to display what ever you wanted.

Good luck.