OK, it's getting quieter here, and I figured out part of the problem.
You're getting double links because your theme layer hack adds the links independently of the CSS, which adds those links in, too.
Hide the CSS version of the footer links with this:
.entry-footer {display: none;}
I got the theme layer code you used working by entering ".entry-footer" in place of the asset divs, but you might not even need that.
It seems that in order to hide links, like the permalink, you need a big chunk of code missing from your theme layer. Let me work on it...I'll get back to you.