Transition from Clerestory Roof to Shed Roof?

[Kbird]

not 100 % sure what you are trying to get actually , the After pic is what I would expect in that situation i think , is the Gable roof not meant to be centred on that portion of the main building? when you "shoved it over" you haven't quite lined it up by the look of the top wall in the plan view. but not sure that will effect the outcome.

is the issue that you don't see walls in the "hacked" 3D image? that is probably cos you use invisible walls right?

M.