B9er,
Since I have not heard the noise you mentioned, so I cannot tell you what may be the cause of it. Have you tried to drive the car with the window down to see if you can id the exact location? One other possible cause may be your wheel bearing going bad. My car always have some intermittent whining noise, and I found out it was my vacuum pump is recharging and hence the noise.
As far as the window is concerned, it should come down an inch or so when you open the door, and then it will go up when the door is closed. Tell the dealer to reset the window. I had to have mine done when I installed a new battery recently (my original battery finally gave out after 6 years) and the window did not close appropriately after that. The Service Manager got into my car and did some quick adjustment and the problem solved.

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95 R129
04 Infiniti G35.5 BS
10 X204