How do I remove Popular Threads from my Top Bar?
Also how do I get the icons next to the class name for the Currently Recruiting area?

With the drop-in template, you'd need to modify the CSS to disable that particular section. Adding visibility:hidden to the CSS rule for that box (#threads) will hide it.

For a complete example, you'll want #threads to be this:

#threads
{
	background:url('http://dkpfiles.com/dkp-templates/bloodelf/threads.png') no-repeat top center;
	height: 93px !important;
	overflow: hidden;
	padding-left: 10px;
	width: 280px !important;
	visibility:hidden;
}

For that, head to Admin > Games, click "Classes" and then from there, edit each class, and you can choose the icon, or specify your own custom ones.

Thanks, worked like a charm