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.
I don't have a picture of the carlines in the clerestory being formed. But, I'd draw one and then transfer it to styrene using the pin technique from the master classes. I used 0.020" and 0.040" styrene for the carlines. What I did was transfer the contour to a piece of styrene, rough cut it on a NWSL chopper, and then file it to match a template. I have some earlier techniques I used also in my photobucket album...the first roof had a couple deficiencies...just like my picture documentation.
For the clerestory sides, I made a point to use 8" scale wide styrene strips to form 8" tall clerestory windows...the window openings may not be quite perfect, but the height is constant...
You may notice that it is an On3 car, not large scale...but the techniques should be fine...just the dimensions would vary. I plan on doing this for some 1:20.3 cars in the future (I've begun building hardware for a Colorado Central way car...with plans for a short baggage car in a year or two).