I leave the OEM cross bars on. The Yakima rack puts inward pressure on the roof rack, so I believe that leaving the OEM cross bars on counteracts the effect of the Yakima .
I don't have a sunroof in my SR5, don't think it is availalbe on the 2004 SR5 models here in Canada.
I have no noise from my roof rack, and associate the fairing as being all or part of it.
Hope this helps