Change your conditionals. There's a myriad conditions your can use to your advantage: in the first case, since you're pulling the parameters off one by one you can check for whether @ARGV still has elements:

my $MISC_FILE_DIR = @ARGV ? shift : die usage();
# ...
# ...
[download]

But I'd rather write that piece as

die usage() if @ARGV < 5;
my ($MISC_FILE_DIR, $req, $inqfile, $sent, $status) = @ARGV;
[download]

Your second situation requires the canonical fix, a test of definedness:

while( my @row = $sth->fetchrow_array ) {
        print join( '|', map ( defined() ? $_ : 'NULL', @row )) ."\n";
}
[download]