Some things you can try with 3 - if you have turned off the auto roofs, go under the roof and see if you can delete and extraneous "supports" that may appear from intersections. Yes, it can be destructive but always remember you have an undo there if something goes wrong! It's pretty much a given that if you find a triangular support inside the center of a hip roof it's probably one of those "intersecting" things that can go without harm - finding a triangular support at anything but the end of a gable roof is most times something that's possible to delete without any harm (and sometimes to more than just problems below).
Another thing I have noticed (since 2) is that when you put a lightning rod on the roof it can give you a gap in the floor below the roof (and thus the ceiling you're building under it). If you move something like this, it will allow you to apply the floor above and then the ceiling below that floor - move the object, fix the floor and put it back. Think of anything "extra" that may be added to a simple roof as a possible im-pediment (LOL).