This is the problem that all of us probably have with the new front windshield rubber. Both upper corners stick out/up. Carefully trim them a little with a long blade razor knife until they will lay flat when the stainless corner moldings are installed. Before you install the corner moldings for the last time, make sure you put a bead of black RTV between the
back of the rubber molding and the roof line such that it fills that gap and prevents water from getting in. Be very careful to not get any RTV on the underside of the corner stainless trim, or you may never get it off again.