I also have a 2010 model and one thing for sure is that the gear box isn't the quietest always been a little clunky, they are robust but it's a clunky one, not the best designed unit for quietness but you do get used it.
As for the water pump, yes they do fail, some people have replaced theirs 3 times, mine just had to be replaced last week!
See how it goes for you with Lexus, if your not happy maybe you can ask for them to take the vehicle back under sale of goods act, hope you get it sorted.
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