A. Carl Hagstrom responds: The evenly spaced ridges of the roofing profile present a real challenge. When visualizing a flashing strategy for the down-slope face of the chimney, picture the plane of the roof at the top of the ridges, not at the lower, flat portion of the roofing profile. At the sides of the chimney, extend the flashing out past the nearest formed ridge, fold it over the ridge, and then fasten through the flashing at the high point of the ridge with neoprene gasketed roof screws.
This goes against the roofing manufacturers’ recommendations to place screws in the flats of the roofing, but I’ve used this approach with success.
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