Thank You Wunibald,
Your example worked perfectly, I have modified it below to be attached to an event so that it applies to every controller/module. To do this I have included it into the onBootstrap function in my Application module.
$events = StaticEventManager::getInstance();
$events->attach('Zend\\Mvc\\Application', 'dispatch', function(\Zend\EventManager\Event $event)
{
$baseUrl = $event->getRouter()->getBaseUrl();
$renderer = $event->getApplication()->getServiceManager()->get('Zend\View\Renderer\PhpRenderer');
$action = $event->getRouteMatch()->getParam('action');
$controller = $event->getRouteMatch()->getParam('controller');
if (strlen($controller) > 0)
{
list($module, $_null, $controller) = explode('\\', $controller);
$renderer->headScript()->appendFile($baseUrl . '/module/' . $module . '/view/' . strtolower($module) . '/' . strtolower($controller) . '/' . strtolower($action) . '.js');
$renderer->headScript()->appendFile($baseUrl . '/module/' . $module . '/view/' . strtolower($module) . '/' . strtolower($module) . '.js');
}
});
Once again thank you for pointing me in the right direction.