Chimney repair & reroofing question

It's time to get the roof redone, which isn't too big of a problem. The roof is very simple (a basic gable and 2 separated, smaller hips) and I'd consider doing much of it myself if it was a more comfortable pitch.
Anyway, I did have one question. The roof is old (1915) and originally was the shake shingles on 1x6 planks. The shakes are no longer there, but the planks remain and are now covered in 4-5 layers of asphalt shingles. My plan is to have the contractor strip down to the planks (which will make a huge mess in the attic unfortunately) and cover them with 3/8 or 1/2 CDX. The only real problem I see is the planks on the overhangs (about 18") of the gable ends droop noticeably so I'm concerned with how the CDX should be attached on the edges. I fear staples or nails would eventually pull away so I was considering requiring them to screw the end pieces.
What do you think? The best way would be to just replace all those boards, but that will involve more work, and we need to keep this inexpensive.
My other concern is the chimney, which has deteriorated quite a bit over the years (we've been here only 10 years). It appears a few decades ago somebody put a coat of mortar over the whole exterior and painted it with a silver colored substance. That has since cracked and pieces have chipped off over the years (I've found several chunks in the yard while mowing). 3 years ago we had a new furnace put in that required a sleeve and they installed a galvanized sheet metal cap over the chimney, which comes down the sides about 4-6". It has never leaked since we've been here (that I'm aware of).
My thinking is I need to have the chimney fixed up prior to the roof being done so no damage is done to the new roof. I was thinking maybe I could get by with either having it rebuilt from roof level up or preferably to just remove the chimney so only the sleeve comes out of the roof (it's just furnace/water heater, no fireplace)? I assume that is all they do when a new gas furnace is installed when no chimney exists. Is that practical?
Thanks, Michael
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I should think that it would actually be easier to take the skip-sheathing and shingles off all at the same time. Just cut all the way down the roof between rafters, and shove the whole assembly off. That's my plan for my roof, anyway.
In any case, unless you have some reason to want the planking left in place, why not let the contracter decide what he wants to do? It's not like he's going to deliberately make things harder.
--Goedjn
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scribbled this interesting note:

This may sound easy, but it isn't. After thousands of residential roofing jobs, we've found it is easier by far to remove one roof at a time and put the debris into the dump truck as we go. Less mess, less fuss, no large, unwieldy assemblies to try to manhandle on an already unstable work surface.

The lathes the original shingles are attached to determine the height of your facia board. If you remove them, you will find you either need to go with a thicker decking to make up that space, or remove and reinstall or otherwise alter the facia board to make things at the eave work out correctly. It is all in the geometry of the original installation.
One advantage of having the lathes on the roof, at least when we remove a wood shingle roof and install decking, is we align the lates so that the plywood decking falls on one of these horizontal lathes every four feet up the roof. This insures a good, strong deck and removes the necessity of altering the existing facia.
If your home has no existing facia then all the above is immaterial, except the part about aligning the lathes and having the plywood decking fall on one of them as opposed to landing in free space.
-- John Willis (Remove the Primes before e-mailing me)
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