The Problem
It seems that you’re using the normal theme template files for posts and pages to display your custom post type. This means, that you also got the wp_head() hook and other template, that output default (post/page specific) things.
The solution
Add a template file to your theme, that’s named single-{$post_type}.php and nothing than the loop with only echo get_the_content() in it. This way you can build your HTML without any interference.
get_the_content() has no filters applied, that normally get attached to the_content().