I recently removed mine and put them in the spare tire area to see if my mpg goes up. No sense in keeping them on all the time when I will only use them one season of the year.
I had the front bar right behind the sunroof, and the rear bar right in front of the rear rail mounting bracket. No noises, even with the sunroof open.
I had the front bar right behind the sunroof, and the rear bar right in front of the rear rail mounting bracket. No noises, even with the sunroof open.