Did you replace upper shock mounts? If no, they are broken. If yes, you didn't tighten them up properly.
Did you put that cone shaped washer on the right way? It should be backwards of the way it seems like it should go.
Did you break or detach a sway bar end link?
Did you tighten everything to torque spec with a calibrated torque wrench?
Best way to find out what's clunking is to jack the car up and start shaking things. Should be fairly obvious when you do that.