When plumbing pipes and chimneys have to go through sloped roofs, they are always cut fairly large just to make sure that the pipe will pass through. The problem is that a 3 inch round pipe needs an oval hole in a sloped roof. There is an easy trick for drawing out the hole.
Hold the pipe in place and run it up close to the roof decking. Then shine a bright flashlight through the pipe from the bottom. If the pipe is at least 3 or 4 feet long, the light coming out the end will shine straight forward, not flair out. Take a pencil and trace the light on the underside of the roof deck. That gives you a perfect oval about the size of the inside of the pipe or chimney. Measure the smallest distance across the oval -- a line parallel to the ridge of the roof. Compare this measurement to the outside diameter of the pipe or chimney you want to put through the roof. Enlarge the oval so that that smallest measurement is about 1/4 inch more than the outside diameter of your pipe or chimney. When you cut out that larger oval, the round chimney will slide out perfectly with a neat 1/8 inch space all around.