//i dont use the session shopping cart quote, instead i will load the inactive quote directly
    //$quote = Mage::getSingleton('checkout/session')->getQuote();
$quote = Mage::getModel("sales/quote")->load($inactive_quote_id);
    $quote->assignCustomer(Mage::getSingleton('customer/session')->getCustomer());
    $quote->collectTotals()->getPayment()->setMethod('payment_method');
    $service = Mage::getModel('sales/service_quote', $quote);
    $service->submitAll();

$order = $service->getOrder();
$order->save();