Hey guys! This could be a long story but I'll keep it short. :) Pretty much my home inspector screwed me by overlooking an OBVIOUS leak in two places!

Anyway, I have a leak in my garage attic around the chimney and also in the house attic around the chimney as well. The garage leak isn't too bad. The one in the main attic is serious. The sheathing is rotted from the edge of the house or the chimney to about the first rafter. I would be very afraid to walk on this without the fear of falling through. Upon inspecting the roof; I don't see any flashing up against the chimney but I believe there is flashing under the shingles. The shingles are butted up against the chimney and caulked around the edges.

Here's the question. I have never flashed before. I believe I understand how to flash a brick chimney from my research but I have yet to come across flashing a rock chimney where there is no uniformity. Would I have to cut into the rock with a rock cutting blade? Any other tips?

Here's a pic of the house and the part I have circled brings up another question. Should that part of the roof have flashing too since the two structures meet? If so, how would you accomplish this with the wood siding?