Hi There,
1.) I am not sure about the changes, but you have change it back.
2.) Can you clarify your expectation here? The code added by @RueNel will only remove all posts under NEWS category from the display on default index blog page. But how it works on single post pages, regardless of categories will still be the same. That is the default structure of wordpress. There’s blog index page and there’s category pages. At the moment, I am not sure what you meant by it also opens on blog page.
4.) and 5.)The code provided on #6 will only work on blog index page here: http://patricklemmer.com/blog/. It exclude NEWS category from display.
By default, category pages like http://patricklemmer.com/category/news/ will only display post with that specific category. We don’t need any custom code to hide other post not included here.
For recent post element, like on your homepage, category will define what is included. It will display all post by default (maximum 4) but we can filter it to display post under specific or multiple categories as defined.
Now, what do you expect with primary cat here? You can add how to, blog or any other categories and it will display anyway by default on blog index page here: http://patricklemmer.com/blog/
For portfolio, how was it before? Are you using Layout portfolio? After checking, I can see you have edited portfolio page using Cornerstone builder. If in case you are set to use Layout Portfolio, the page content will use the template to list portfolio items and builder is not necessary. Please also clarify the changes that has been disappeared. Thank you.