Prevent author role from editing all posts in custom post type?

You should declare your desired capabilities when you are registering the post type.

Justin’s article here is a good one for custom post types:
http://justintadlock.com/archives/2010/04/29/custom-post-types-in-wordpress

When you are registering your custom post type, you can set this to be standard capabilities for posts, eg:

'capability_type'    => 'post',

or to be standard capabilities for pages, eg.

'capability_type' => 'page',

or set your own capability type, with global controls or get right down to the specific controls through a specific array, eg.

/* Global control over capabilities. */
'capability_type' => 'super_duper',

/* Specific control over capabilities. */
'capabilities' => array(
'edit_post' => 'edit_super_duper',
'edit_posts' => 'edit_super_dupers',
'edit_others_posts' => 'edit_others_super_dupers',
'publish_posts' => 'publish_super_dupers',
'read_post' => 'read_super_duper',
'read_private_posts' => 'read_private_super_dupers',
'delete_post' => 'delete_super_duper',
),