I am having the same light vibration feeling in the brake when stopping at low speeds. Had to tech look at it during the 1k service (done at my home) but I think I will have actually take it in to have them document and isolate it. I haven't noticed engine noise.

 

I just read your message about the whirring or whining on initial acceleration and shiftng and my 2013 ES350 exhibits the same problem. It is most audible in the lower gears especially from a standing start. I purchased in Nov 2012 and now have 1800 miles on the car. It was not there at first but developed over the last month. I have not taken it in yet but the noise is very annoying, especially for a lexus. PLEASE LET ME KNOW IF YOU FIND ANYTHING OUT.
Thanks,
lexsbob