The way I suggest you handle this is to allocate the sales price amongst all the assets related to the house. For example, Lets say the sales proceeds were $206,000, the cost basis of the house was $100,000 and the cost basis of the land was $50,000, you would allocate the proceeds as follows:
Roof & Skylight - $5,075
Land - $50,000
Building - $150,925
This will result in no gain on the disposition of the Roof or the land, and all the gain would be on the building. You could also allocate the proceeds on a pro-rata basis, but the total gain will be the same.
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