The clean looking mounds are formed sheet metal for strength. The other mounds look to be silicone installed from the factory for some reason. My LJ had the same thing, but not near as much, and I just prepped them really well and have had no issues. Here is a pic. The Monsta in mine is holding up great and I haven't had my top on for two months.
2005 Unlimited Rubicon, too much junk to list!
My build: [url]http://www.jeepforum.com/forum/f22/unlimited-bottomless-pit-build-1241399/[/url]