@MartinH81
As I've say you are on the right way.
Few remarks:
1. You've modified the shape of the hole room in that way it exceed the middle of the roof. Is not what you've present in your previews post.
2. I've say to set faces around the hole at 90. You forget the face 8.
3. You could make multiple holes by drawing and selecting multiple rooms with this destination.
4. You don't need another way to fill the gaps. Just draw the holes (rooms) correctly.
5. DON'T use the global "Modify texture" but "Modify materials" and there set the textures for every face and border.
Other wise your results will look ugly as in your last 2 picture.