Multiple Loops break Pagination

I’m working on a category template that organizes posts into two columns using multiple loops, with an additional loop for a top featured area. But of course that makes the pagination not work! I’ve read a few things about plugins and such but nothing’s seeming to work with this one.

This is the code with the two column loops…

[Code moderated as per the Forum Rules. Please use the pastebin]

Any help is greatly appreciated!