Curious, how does the roof lifting mechanism work? it looks like it's not factory and that could lead to misalignment when you lower the roof which can give you issues with water intrusion while driving. Could just be the photos but one of your before pics with the roof down seems to show a significant overhang of the roof to the camper. I know folks have had issues with driving in the rain but not while popped up that are usually attributed to how it is held down in front.
Otherwise, I agree, way to tackle that roof!