Attached is a .patch file for modifications made so that CartThrob OrderManager (8.1) sends emails.
File: system/user/addons/cartthrob_order_manager/mcp.cartthrob_order_manager.php
A particular fix:
// 'message_template' => $notification['email_template'], CARC BUG FIX key is $notification['template'] NOT $notification['email_template']
'message_template' => $notification['template'],
Kudos to Greg Crane.
order_manager.patch
Maybe Carthrob 9 fixes some of this.