I too have the same front pssd wheel sqeaking. I checked the fender issue out too. That wasn't it. I pulled the wheel and found nothing. I cleand the rotor also. no change. Off to the dealer this week to find out..drives me up a wall. 1100 miles.

 

2012 JKUR with 500 miles and I have the squeak too. Rear passenger side. Also most noticable when driving past divider or fence. Here's how I fixed it...

...reach down on the dash and find large round knob, push it, then turn it to the right.

Just kidding. It's annoying as hell. I looked around and couldn't find anything that looked like it was rubbing. Definitely sounds like its related to the rotation of the wheel though. I plan to take it into the stealership when I get a few spare minutes. Subscribed in case anyone beats me there and it's a simple fix.

Edit: to OP...sorry no advice on the clunk. I have an auto.

 

Picked up the new 2012 Rubicon and the left front rotor splash shield was rubbing the front rotor, bent it back no more noise.

 

I have a 2012 jku rubi...annoying noice coming from passenger side over 20 mph...sounded like a brake squeak...ended up being a bent passenger side rear axle...told its not safe to drive...part on order...gotta wait 4 days...driving a 2011 avenger rental...boo hoo

 

Whew! Glad I bought a 2011 that doesn't squeek! And guys, there are good reasons not to buy a first model year vehicle.

 

At least wait a few months until a few of the bugs and recalls get worked out.

 

Haha, few months??? They still aint got the bugs and recalls worked out on the 07's.

 

Yeah, what he said!

 

Just got back from the dealer with the Jeep and they couldn't get the squeak to repeat. The drove it next to a line of cars as I suggested to get the noise reflection and didn't hear anything. They also pulled all 4 wheels and checked to see if anything was rubbing or loose and couldn't find anything. I'll drive it later to see if I can hear it again. They said it might have been something that got stuck and has since fallen out. Also, they said the clunk was normal. 250 miles.

 

could not duplicate...go figure.

It seems is starts once I've been driving around a while. I'm nto sure wha tyou guys are finding if it does it all the time or after driving for a while. I'm going to pull the wheel again and check things out in there one more time. Annoying as hell!