Installing Roof Jack in Shake Roof
Since Cedar does not flex and bend like composition shingles, they have to be removed.
To do that, you have to go to a roofing supply house and purchase a tool called a slate nail ripper.
It is a double 90* bend on the handle and then a long flat metal shaft that slides under the shakes or tiles. The tip of it is curved and wider than the shaft. It sort of looks like a mushroom head. When the bottom portion goes past the fastener, you can hook onto the fastener with its cutting edge.
When you get it tapped in far enough under the cedar to where the nails or staples are located, you slide it sideways until you feel that it has encountered the nail or staple. Then you take a hammer and tap downward, meaning towards the gutter eave edge on the vertical portion of the handle.
You continue tapping with the hammer until the fastener either shears off from the cutting edge of the ripper, or it begins to pull it out sideways.
Continue with as many courses above the location until you have the necessary room to install the pipe flashing.
I am assuming you know how to install the flashing properly, since you referred to composition shingles and it seemed like you know what to do once you get to that point.