Clunky shifts usually indicate weakness in the compensator feed and exhaust backfill hydraulic circuits inside the transmission. Those two circuits regulate shift timing, feel and prevent centrifugal apply of the front three clutch packs in the transmission.
If subsequent tuning doesnt resolve ( it likely wont) but it doesnt get any worse, just drive it. However if you start to notice the clunks get more frequent and/or harshness increases, next step would be a full diagnosis to include electrical, vacuum testing of the TEHCM and Valve body assemblies, respectively. Speed sensors would also be checked...
