When coming to a complete stop, its starting to make a clunking sound. and sometime at a certain speed it has a little vibration. could this maybe be the drive shaft or U joints ?

 

The vibration could be as simple as imbalanced tires or alignment issues. I wouldn't start with tearing apart u-joints . The clunking noise you are describing might be the sway bar or bushings... I know the noise is a common problem, don't remember exactly what it is. Is yours a sport RR or a full size?

 

It's a full size. I know that it cant be the tires ( they are new ) the alignment just done.

 

I had same problem with clunking sound,it was the transmission.It was down shifting to hard. The dealer reprogramed the tranny when it was under warranty and fixed problem. I also had a vibration at certain speed, come to find out it was a flat spot in the tire.