Not sure if this is the right place... but line 496
$nopages = "AND $wpdb->posts.post_type = 'post'";
seems to be the only place I see any post selection limited to just post
When I've messed around with other plugins, to add in CPTs, I'v elooked for similar selection criteria. And added in my own CPTs. So the first place I would mess around is here. I'm not a coder, so I'm not sure exactly how to add in the CPT here....
$nopages = "AND $wpdb->posts.post_type = 'post', 'cpt', 'another'";
or if it has to be in an array
$nopages = "AND $wpdb->posts.post_type = array( 'post', 'cpt', 'another' )";
, or what.....
I'm sure you know to have a backup available, and that if you get the syntax wrong, you could kill the plugin, or your site. But as long as you can ftp in, no harm no foul really. I know I've killed my sites a few times doing stuff like this. Its why I have a dev install of WP that is pretty much a copy of my live site.... so I can poke it with a stick to see what happens