If you have selected the custom post type in the wp-discourse ‘Post Types to Publish’ option, it should publish to Discourse without any problem. I’m not sure what could be going on with that.
I will make a change to the wp-discourse plugin so that post content is only republished to Discourse if an ‘Update Discourse Topic’ checkbox is selected on the WordPress post_edit page. If you don’t want to have to manually update posts on Discourse to remove shortcodes, you could probably remove them on WordPress by using the first function in the Dealing With Shortcodes section of this topic: WP Discourse Plugin Tips and Tricks (it will remove anything that looks like a shortcode, but leave any content that occurs between the shortcodes.) You could possibly also use that function to add some keywords to the excerpt.