The easiest way to have custom HTML per post is probably by using post type templates. You can easily put those into version control.
As for the CSS, you could create separate files per post as well. But this harder to maintain and leads to more stylesheets that need to be downloaded by the user when they browse your site. I’d usually put all the different styles into one CSS file. This way, the browser only needs to download it once and then it will be cached.