Kassey here from the Shopify Guru Team! I'm afraid there isn't a way to insert a different message per customer via the order confirmation notification - however, you do have the option of sending a custom email to your customers via the Shopify admin. What you can do is click on the customers name via the order page or via the customer section from your admin, you will then see a "Contact" section on the customer page on the right hand side. You can simply click on their email address (it will be in blue text) and from here you can send your customers a detailed email.
I hope this helps, but if you have any further questions - be sure to reach out to Shopify support!
Sorry I may not have explained myself clearly.
The message can be the same for every customer. What we need is a message that is sent based on the product purchased. In other cart softwares it was called Special Instructions. We need a way for customers to receive speciual instructions when they purchase a specific digital product.