Ken
I did pretty much what you are asking.
I used OSB roof decking (tech shield from Home Depot) on mine. As long as you have a good insulation barrier ( I have 4 different layers) then there are no worries about the roof. As an added precaution I used the tech shield because of the foil covering, foil side down. Probably not needed, but it was cheap insurance. Try putting your hand on the shingles on a hot summer day, OWW! It is alot hotter than the inside of my oven will get.
You are right about the chimney pass thru, I could not find one anywhere either, so I made one. I cut the wood so it would be 8 inches away from the chimney pipe. Then I used metal flashing to cover most of the exposed gap, leaving about 1/2 inch space between the chimney and flashing (being cautious again). I should add that while doing the curing fires I put my hand on the outside of the Duratech to see how hot it would get. That Duratech is great stuff as it did not get more than warm. Then down went the felt paper. Next, I cut some scrap cement board onto 4 rectangular pieces, two notched for the peak of the roof, to make a box (fake chimney) around the pipe, if you can imagine what I mean. Screwed the "fake chimney" to the roof. Bought a tube of fire barrier sealant and filled the inside gaps of the box. After that set-up I finished filling the chimney with the LaHabra Wall (stucco scratch coat) till I had it flush on top and then sloped it just in case any water from rain got under my cap. Then shingle and stucco the outside of the chimney.
Held up great so far.
I hope that is a good explanation.
