Not your real problem I know, and you are aware that it is sub optimum, but:

my $thr1 = threads->new(\&process3, 0,$endline, "c001n05");
my $thr2 = threads->new(\&process3, 0,$endline, "c001n06" );
...
$thr1->join();
$thr2->join();
...
[download]

just calls out for either a hash or an array:

my @thr;

for (1..$numThreads) {
    push @thr, threads->new(\&process3, 0,$endline, sprintf "c001n%02d
+", 4 + $_);
}

$_->join () for @thr;
[download]