Remove the old roofing down to the plywood and flashing. Pull old shingles from the roof by prying them loose. Drive a nail puller under each one with a hammer. Inspect the roof, replace any damaged plywood and contact a contractor if any of the structural trusses are damaged.
Inspect and repair the flashing. Cut new pieces of tin flashing with snips. Remove the old flashing with a nail puller and hammer. Nail the new pieces of flashing in place with roofing nails. Caulk the seams around each piece of flashing with silicone. Wipe excess caulk away with a wet rag.
Unroll felt across the roof. Cover the bottom edge of the surface with the felt. Cut the felt to fit the length of the roof with your razor knife. Staple the felt in place. Unroll the felt above the strip you just fastened. Cut the new piece with your knife. Overlap the top of the first piece of felt with 6 inches of the new piece. Staple the new piece in place. Continue this process until the roof is covered.
Open the bundles of cedar shakes. Inspect each one for deformities that will make it unusable. Push shakes into your table saw to cut them in half lengthwise. Cut about a quarter of the shakes you have on hand to get a good supply of half-shakes.
Install the first layer of cedar shakes. Alternate full and half-size shakes on each row. Place shakes from the bottom to the top of the roof. Nail each shake in place with two of your 8d finishing nails. Take your time, make the corners tight and stagger the breaks between shakes from one row to the next.
Install the second and third layers of cedar shakes. Stagger each row so that breaks never line up with those in the previous layer. Caulk the perimeter of the top layer, including the corners, with clear silicone. Wipe away excess caulk with a wet rag.