Well, props to mafd2 for pointing me in the right direction.
I FOUND what was rattling. Its a little metal cam piece in the hinge mechanism of both rear seats. If the seat is all the way up its engaged, as well if its all the way down. Since my sub box is just barely not letting the seat sit down all the way (even moved forward), its free to rattle.
See pics below.
Now what to do. There really isn't anyway to tighten it as it's put in via a rivet, and there is really no way to drill in out and replace with a bolt to tighten it. Its pivoting on the rivet. My plan is to lift the seats so they will sit down all the way. I had to do this with my previous truck (which was a Ford and the seat wouldn't lock down). I plan to place a few flat washers (appox 1/4in thick) under the seat brackets and give it a shot. Will update when I'm done tomorrow.