As in question, excluding node fields from HTML print page is easy via CSS, but what about PDF version (PDF version module)?
You should create a new suitable view mode or re-use one you already have. This allows you to control the settings with the Field UI, while still allowing you custom templates if you need to.
You can try overriding the print template (print.tpl.php). The default template for that is in the directory of the print module. That's if you're using Drupal 6.