The house was large, constructed of white clapboard and sections of stone with black doors and shutters.
Does it mean that the walls were partly covered with white boards and partly they were bare.
Or maybe the walls were covered by white boards and some other parts of the house were made of stone?
Most of the house was made of wood with clapboard, but parts were made of stone. The clapboards do not cover the stone.
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.