This one just struck me that when creating new mail merge template Sales Order does not appear as entity in the list…
Following article will help you enable mail merge of any CRM entity.
Again note that this is unsupported way to add this sales order entity in to the list as mentioned in steps below…
Step 1: Export Sales Order Entity customization from CRM Environment
Step 2: Open Customization file and then Update (or Add) IsMailMergeEnabled as 1, Save the changes.
Step 3: Import the changed file in to CRM and publish the changes.
If above method does not work then try following unsupported method, connect database and run following query, change entity name as per your requirement..
Hope this helps..