Struggling with extended gable roof and ceilings

[JoAnn]

1. Your second floor should look like this 2D example. That will also fix the exterior wall problem.

2. When looking at your real pic and your 3D pic, the ceiling heights appear to be wrong.
Floor 3 ceiling should be set very low (which you can raise after roof is correct and "auto build roof"
is turned OFF.
In my 3D example, I set all 1st floor ceilings to 96".
On the 2nd floor, the left wing is also set to 96". I set the right wing at 68", and the 1st floor shed roof then perfectly attached itself to the upper roof.
So, experiment with the finished ceiling heights and see what happens.