The clunk is pretty likely to be the rear diff mounts in the subframe... this is a pretty common failure. I've never changed them though, and I don't know how hard it is. I know there is a special tool to pull/press the new ones in. Usually when the diff goes bad, it howls, not clunks. Don't use the 300E diff, the ratio is not the same (see PDF link above), and besides I don't think changing the diff will do anything.
