in my experience, clunks come from odd places.
like cracked spider gears.
worn shock mounts allowing the rods to pop
i have had worn cv joints produce a clunk, and in the trash they went.
dangernoodle had a loose diff to xmember bolt
i've had problems with exhaust pipes slapping the underbody in the 04, which needed some poly engine mounts to fix
sometimes i think if i left the cars stock and babied them, they'd never make odd noises. but, they can be found and fixed. it's not always the obvious places.