The rust is on the ledge you talk about (where the weatherstripping snaps back into place on the metal) - underneath there.
I kind of eyeball the measurements without a problem. I think it was something like 5" back from the edge of the windshield (pretty much right above the front of the sunroof for the cross bar), and 27" inbetween the Q towers. But if you have the measurements provided by Yakima, yes it does put you fairly far back on the roofline. The back Q towers seem to fit slightly odd on our cars if you follow their measurements - I'll try to snap a picture with the rack on the car.
