Dan - I actually use a Baja Megamule rack (
http://www.bajarack.com/the-mega-mule-1) on the Yakima crossbars. It is easily removable, sturdy, has a built in wind fairing, and has good expedition type accessories (although I so far only have a shovel bracket). When not in use it hangs from my garage ceiling. It can't stay on all the time because our office garage has a 6'-6" height limit and the truck is almost 6'-10" with the rack. This is the lift I am using:
http://www.racorstoragesolutions.com/p/detail/phl-1r?AspxAutoDetectCookieSupport=1. I don't use the tray and just hang the rack from the cables. You probably could leave the bars on the rack but would need to check the clearance when the garage door opens. It probably would not work in my garage so I just leave the crossbars on the truck.
I ordered my truck with the standard short roof rails and the Yakima landing pads fit perfectly.
The fairing works OK. You still get some wind noise but that is probably to be expected.
Regards,
David