It sounds like a defective electronic component in the transmission, or a defective ECM (engine control module--which controls engine functions. These components have been reported to be defective in all Toyota from about 2003 on when they began installing them unknown to the public to save money. ECM runs up to $2000, a failed transmission could be a bit worse. Clunking and poor shifting--if the transmission itself is not failed is often a defective electronic component, and Toyota makes their components over seas in factories which pay very poorly. This saves Toyota big money...unfortunately it also costs the consumer big money because they often fail after the warrenty has expired. Good luck.
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