Hi,
That's actually quite easy to do.
Edit the email via the menu Display>Emails.
There, if you just want to add text and the stock level, you can add such text in the HTML version:
Stock for that product: {LINEVAR:product.product_quantity}
after for example the tag:
{LINEVAR:PRODUCT_DETAILS}
If you want to add custom PHP there, you can write it there inside PHP tags.
For example:
Stock for that product: {LINEVAR:product.product_quantity}<?php echo 'test'; ?>
Otherwise, for more complex modifications, you can also add custom code in the preload of the email.