Clunks from inside the exhaust manifold may be crumbled pre-cat elements. Use a mechanics stethescope (or big screwdriver) to listen for the source of the noise. When the pre-cats start falling apart the dust clogs up your exhaust and bogs down the engine. The cold engine bogging sounds more like an IAC or loose hose problem in the intake area. You still may have clogged up EGR ports behind the throttle body which can be cleaned with carb. or TB cleaner and a soft rag once the TB is removed. If the EGR gets really bad, it usually causes a CEL.
