Position the new stove where it will be installed. Position one section of chimney pipe at the stove connection to use as a guide and use a plumb bob from the ceiling to mark the approximate center of the chimney pipe on the underside of the roof sheathing plywood.
Drill a ...-inch pilot hole through the roof sheathing plywood and metal roofing to mark the chimney hole's center.
Use a drawing compass to mark the outside diameter of the hole for the chimney assembly on the metal roofing's exterior surface according to the manufacturer's specifications and the clearance mandated by the building code. Usually a minimum clearance of two inches between the chimney pipe surface and any wood or other combustible material is required.
Use a jigsaw with a combination blade to cut the chimney hole in the metal roofing and sheathing plywood.
Position the chimney's roof flashing over the hole cut. Slide the flashing down approximately three inches and scribe a pencil line across the top edge of the flashing base. Use metal snips to cut across the line marked to the width of the flashing base plus ...-inch on either side.
At the line just cut, slide the top edge of the chimney flashing beneath the metal roofing and roofing paper. Slide the flashing into position over the chimney pipe hole. Raise the metal roofing slightly to run a ½-inch bead of exterior grade caulking across the top of the flashing base approximately ½-inch above where the end of the roofing will sit over the flashing surface.
Run a ½-inch bead of caulking under the perimeter edge of the chimney flashing base where it will rest on the metal roofing's surface and press the flashing into place.
Assemble the wood stove's chimney pipe sections according to the manufacturer's instructions. Slide the chimney assembly through the roof hole and the chimney flashing's collar. Position the lower end of the chimney assembly on the wood stove's chimney flange and secure. Use a builders level to ensure the chimney assembly is plumb above the roof surface, and secure the roof flashing in place with insulated roofing screws. Keep the screws to each side of the flashing and to a minimum to hold the flashing metal flat against the roof surface. Do not screw across the bottom edge of the flashing.
Install the the chimney cap to the top end of the chimney assembly according to the manufacturer's specifications.
Run a bead of caulking down each side of the flashing and around the gap at the flashing collar for added waterproofing.