I can see you've been a cedar-shake-scribing fool as well. So worth it. The filler piece that was the transition from the old clapboards (?) to stone is nowhere near as clean a look. And I don't think that losing some of the depth of the stone reveal is a loss in any way----certainly not in exhange for the shakes.
A cup hook (or a 2.5" finishing nail) and a second ladder would help with the chalk lines. Scaffolding and planks are for poosies. (I'm guilty of skywalking, too, but Mark is on point---way safer and more maneuverability.)
What's going to happen to them after the installation is finished? You've been doing great so far, so don't piss me off now.