Magento – Hide “Grand Total (Excl.Tax)” and “Tax” in order email

To calculate and process the grand total you need to follow these

$quote = Mage::getSingleton('checkout/session')->getQuote();
    $address = Mage::getSingleton('checkout/session')->getQuote()->getShippingAddress();
    $address = Mage::getSingleton('checkout/session')->getQuote()->getBillingAddress();
    $quote = $address->getQuote();
    $session= Mage::getSingleton('checkout/session');    
                $items = $session->getQuote()->getAllItems();
        //$items = $quote->getAddressItems($items);
    //echo '<pre>'; print_r($items);

    if(Excellence_Fee_Model_Fee::canApply($address)){
                 //$exist_amount = $quote->getFeeAmount();
                    // $fee = 1000;
                        //$fees = $fee * $result;
                    $balance = 1000;
                        //          $balance = $fee;

                        //$this->_setAmount($balance);
                        //$this->_setBaseAmount($balance);
                        $address->setGrandTotal($balance);

                        $address->setFeeAmount($balance);

                        $address->setBaseFeeAmount($balance);
                        $quote->setGrandTotal($balance);
                        $quote->setBaseGrandTotal($balance);
                        //echo '<pre>'; print_r($quote);
                        $quote->setFeeAmount($balance);
                        //echo '<pre>'; print_r($quote);

                        $address->setGrandTotal($address->getGrandTotal() + $address->getFeeAmount());
                        //echo '<pre>'; print_r($address);
                        $address->setBaseGrandTotal($address->getBaseGrandTotal() + $address->getBaseFeeAmount());
                        //$address->getGrandTotal();
                    //echo '<pre>'; print_r($address);
                    echo  Mage::getSingleton('checkout/cart')->getQuote()->getGrandTotal();

This is working on checkout and cart page to update the grandtotal. Hope this will help you and you find a correct solution.

Try to comment the following line from:

app/design/frontend/[interface]/[theme]/template/tax/order/tax.phtml:

<td <?php echo $this->getLabelProperties()?>>
    <?php if ($this->displayFullSummary()): ?>
        <div class="summary-collapse"><?php echo $this->__('Tax'); ?></div>
    <?php else: ?>
        <?php echo $this->__('Tax'); ?>
    <?php endif;?>
</td>
<td <?php echo $this->getValueProperties()?>><?php echo $_order->formatPrice($_source->getTaxAmount()) ?></td>