Hi,
Well, if you're a developer, adding the link in the email should be a piece of cake. You can get the data of the order in $data->cart when you're in the HTML version of the email.
Like for example: <?php echo $data->cart->order_id; ?>
Then for the custom page where you can have that purchase order number form, it's up to you what you prefer. I would personnally develop a really small component (
docs.joomla.org/J3.x:Developing_an_MVC_Component
) where I would have one controller to handle the display of the view for the form and the saving, where I would basically write a MySQL query to store that in the order.
But if you're not familiar with component development, you could use something like a custom HTML module and the loadpoisition plugin of Joomla to basically add your form in a Joomla article, and then have a small system plugin to catch the submit of the form and do the MySQL query.