While braking with the JK out of gear(Its a standard) I can hear an audible clicking coming from the shifter area and I can feel it in the stick. The clicking slows as I go slower and stops when the vehicle comes to a complete stop. its not very loud but its there.... Any help would be great.... thanks Scott

Here are some vehicle stats. 2008 unlimited rubicon, 1.75 in leveling kit 3/4 rear spacer 16,000 miles

 

Are you depressing the clutch while stopping or only using the brake pedal? It is probably a throwout bearing noise, regardless.

 

If the noise stops when the vehical stops, I'd be looking at driveshafts first.

 

Yes I'm depressing the clutch and breaking when I get the noise....

 

I had a clicking noise coming from my jeep. it turned out to be a bad cv joint on my front drive shaft. The boot was torn and I lost most of my grease

 

Your post is very confusing. At first you said you were braking out of gear, which to me means you are in neutral. Then you stated it happens when braking with the clutch in. Do you always press the clutch in when you brake? Does the noise happen when you depress the clutch and don't brake? Does it happen when you brake without depressing the clutch? You need to narrow down the issue in order to get an answer.

 

sounds like he does all 3.
he brakes out of gear and presses clutch.

im gonna say driveshaft boots as well