Might I suggest a slightly different approach:
First, cut out roof supports of the desired contour. (carlines)
Second, set up your clerestory windows above the carlines
Third, at connectors between the carlines.
fourth, glue either 0.010" styrene to the supports at the joint of the clerestory or one end of the clear story...if using thin brass, glue it instead.
fifth, after the glue has dried, wrap it over the carlines and glue.
sixth, overlay additional layers. 0.010" styrene is really nice for this as it bends easily...just be careful of adding too much solvent.
seventh, trim up the sides and apply your roofing surface.