To add Custom Record Type to the list of Field Types in Email Templates follow those steps:
1) Go to Customization>List, Records & Fields>Record types
2) Click your Custom Record Type
3) Mark the checkbox Enable Mail Merge
4) Save the record
5) Log out from the account and log back in
Now if you go to Documents>Templates>Email templates>New you are able to see the Custom record type in Field Type drop down list.
It is now also possible to select the custom fields of this Custom Record Type and add them to the template.