Hi again,
I've been poking around with the roof thing and I also adjusted the hallways, modified the floor layout and so on... I am now able to get the roof on and the project is in final stage. You can check out the pics in this link:
http://www.blackpenguin.org/blog/post.php?idpost=13
I will give you a link to the updated SH3D file, but I just did not have the time to put it out there. Thanks!