My RX330 exhibited the whining and clunking problems (when slowing down). After a few complaints and showing them some postings on this board, they applied a fix that hasn't been made official. The fix includes a "spacer" which adds room between the transmission line and the vehicle chasis. The purpose is to shield the line so the whining noise is not evident inside the cabin.
As with the clunking problem, the fix is to apply TSB004 or greater, reset the ECM's learned values AND use premium gasoline (91 or better). I was using 87 all along, even after the TSB004 update. Finally, I was told to put in 91 octane AND have my ECM reset. Tried it, and the clunking noise went away.
The third problem -- shifting hesitation -- is by design. Yes, like many others, I have adjusted and learned to deal with it. Typically, when I drive at freeway speeds, I have no problem passing. The vehicle provides plenty of power for me to pass effortlessly without "flooring" it. I would agree though that electronic throttle control is something that needs improvement.
