I have the automatic Limited with 35k miles. When I a am slowing down the transmission makes a clunking noise. Not all the time though. It feels like it is downshifting when coming to a stop.
Also I have noticed a loud rumbling sound when slowing down (just on certain roads) coming
from the rear tires. This particular noise sounds more like the tires to me. If you have gone over safety strips on the side of some highways the sound is the same. My CF is lowered with the Eibach lowering springs and I am using the stock shocks. I also have rear 15mm spacers.
Recently I went from 33lbs air pressure to 35lbs of air pressure in all four tires. I have aftermarket wheels and non-stock tires. Tire size is correct for all four tires.
I looked this up on the forum and found similar issues with other owners. Mentioned was the possibility of a loose suspension. Also the driveshaft support and bearing. Needwings carries these. The transmission seems alright in terms of regular driving. Doesn't shift rough or clunk while accelerating. Not yet anyway.
I also have more HP with the TVT 265 kit installed. This just started and I would like to take care of it early before it gets worse. My warranty is up. It will have to come out of my pocket.

 

The noise is most likely coming from the latch on the rear door. There is a TSB out for the dealer to fix it. Or you can do like most people here have done and wrap electrical tape around the latch catch.

 

I took care of that with the tape fix along time ago. This rumbling is LOUD and sounds like it's coming from the rear tires. The same sound you get when you drive over safety strips on the edge of some highways.The tires,springs,wheels,spacers have been on my CF for 5 months. This is the first time these sounds have occurred.
The only thing different recently is the tire pressure. From 32lbs to 35lbs on all four tires.
Tire sizes are correct.

 

It sounds like the CV joints on the halfshaft. Though it could be the carrier bearing. Or even the carrier/pumpkin. What year is your car, and how many miles does it have?

 

If the sound is loud and there is rumbling, and you have aftermarket wheels, I would check to ensure the front and rears are centered correctly. On my front 20s the hole for the hub is a little larger than the hub itself and if they are not centered perfectly, I get vibrations and humming on different surfaces to varying degrees. May not have anythiung to do with your setup, but I would check....

 

36k.2004 Limited. Seems to early for these to go bad.