Magento – How to replace the subtotal including tax with subtotal excluding tax in the pdf invoice

First of all, copying files that can just be overridden from the Core to Local is not best practise as it can possibly give you more work when upgrading Magento.

I have tested your case and found your solution:

First of all I rewrite it in my own extension:

 <models>
            <sales>
                <rewrite><order_pdf_items_invoice_default>MycompanyName_Myextensionname_Model_Order_Pdf_Items_Invoice_Default</order_pdf_items_invoice_default></rewrite>
            </sales>
 </models>

Then I override the function you mentioned above:

 $options = $this->getItemOptions();
    if ($options) {
        foreach ($options as $option) {
            if ($option['value']) {
                if (isset($option['print_value'])) {
                    $_printValue = $option['print_value'];
                } else {
                    $_printValue = strip_tags($option['value']);
                }
                $values = explode(', ', $_printValue);
                foreach ($values as $value) {
                    $lines[][] = array(
                        'text' => Mage::helper('core/string')->str_split(strip_tags($option['label'] . " - " . $value), 40, true, true),
                        'feed' => 40
                    );
                }
            }
        }
    }

What I have done here is just removed the part where you draw the label and added it to the part where you print the value.

If you have long labels/values and you want to keep it on one line, I would increase the value in str_split.

I think you have any extension installed which does the PDF rendering for you rather instead of the touched file? just throw a die('test') into the file and you will know.

Beside of this I can recommend Firegento_Pdf which offers a great event for exactly this:

https://github.com/firegento/firegento-pdf/wiki/FAQs#how-can-i-add-notes-to-the-pdfs-programmatically