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in all, Id guess your just now noticing the noise, not that its new.
x1100
the Z is a very loud car. ive owned 3 350Zs, and as much as i appreciate the car being a true sports car with minimal sound padding, all that road noise can get to you, and the sound of air coming in through the windows, as if they werent sealed right, has been on all 3 of my Zs.
highly doubtful....the window, even when all the way up, doesnt come close to hitting the paint.
and if they took your door panels off than they more than likely didnt mess with the up down mechanism.
Let us knwo what the dealer says.
Here is what the manual says about the windows hitting the top of the car when the battery is removed:
CAUTION
When the battery cable is removed from
the battery terminal, do not close either
of front doors. The automatic window
adjusting function will not work, and the
side roof panel may be damaged.
I would suggest Nissan did not make the windows roll down slightly to make it easier to open and close the doors. That is a good side effect, but the real reason is so the window will not touch the top panel.