The clunking and jerking could be engine relayed, the engine miss, mounts. . Too much oil in the transmission causes shifting problems. The high level will get into the gear train, the drums and planetary will aerate the oil, causing oil pump cavitations. Not good for a hydraulic system. Neutralizing at a stop could be a plugged Tran’s filter or a broken, leaking B2 piston.

Fix the engine problem first, then do a transmission service. Removing the pan will show the condition of the transmission.