Clunking when braking

Hey guys, I have an 06 Prius and this problem seems to be getting worse. Often times when I press the brakes I am having a clunking noise coming from the engine bay. It does not happen ever time that I press the brakes but it does happen most times now. The clunking cannot be felt in the brake pedal or the steering wheel, but it is quite loud. I don't know these cars well enough to know if this has something to do with the regen braking system or not. The CEL light is on in the car for a catalytic converter code. The only other thing I have noticed that may be out of the ordinary is that when the ICE turns off at a stop it is quite noticeable, it seems to shudder and the car shakes a little bit. This is my first Prius and I bought it in non running condition, so I am not sure what the normal is. Since owning the car I have replaced the transaxle, but beyond that I have only done normal maintenance. Any troubleshooting advice?

 

Possibly, I will check that. I should also probable describe the noise more like a popping noise rather than a clunk. It sounds like something popping from out of a bind. It does not always happen as soon as I touch the brakes. I can push the brake pedal sometimes and it will happen right away. Other times it will happen mid braking, I can push the brake pedal and be slowing down and it will make the popping noise before coming to a complete stop.

 

I agree, I think it should be smoother than it is. I don't really think the ICE shaking issues has anything to do with the popping noise but I just thought I would throw it out there incase it does. My plugs are new and the throttle body has been cleaned out recently.