#!/usr/bin/perl -w

use strict;
# ...
use Win32::Exe;

# ...
my $console=0; # originally from script arguments
my $stub="stub.exe"; # originally from script arguments
my $out="out.exe"; # originally from script arguments
# ...

my $exe=Win32::Exe->new($stub) or die "$stub: $!";
$exe->SetSubsystem($console ? 'console' : 'windows');
$exe->write($out);