Multiple loops conflicting with pagination

I’ve spent all day trying to figure this out; looking for different codes and methods to resolve it, and despite the huge amount of results I’d found on the forum, I still can’t seem to get this right.

What I’m trying to do is create a pagination for the following layout:
1. Posts from category #1
2. Loop (excluding posts from categories 1 & 2)
3. Posts from category #2
4. Continuation of the loop (excluding posts from categories 1 & 2)
5. Pagination

So far when navigating through the pages, the results of the loop on the first page are gathered again on the continuation of the loop in the second page. In other words, I’m getting repeated posts -although not duplicates on the same page- that aren’t in the descending order I want them to be in.

I’m not quite experienced in PHP to begin with, so bear with my messy code.

This is the current code I have in my Index.php:
https://pastebin.com/JbPF4h9b

And here’s a link to the current address of the uploaded theme:
https://www.alleviatedmedia.com/lifeartbreak

Any help at all would be greatly appreciated.