Hi Doug,
You can replicate the function of the Main Menu block with the Section block, which is configurable per instance. To display the contents of the Main Menu block in a course, configure the block and change the course id to the frontpage id (usually 1), and the section id to 0.
The availablility of any block is controlled by the "applicable_formats()" fuction found in "mysite.com/blocks/blockname/block_blockname.php".