Thanks all, the copy paste method is exactly what seems to work. I hadn't realized that you could paste a poly into an edit group window. Invaluable.
I still end up with a lip where the roof faces join, as the roof remainder is cut square to the ground plane. This is helped by overlapping the roof faces a bit, as I had to do when I used the "create roof face" command set to a specific pitch, the peaks aren't perpendicular to the ground plane. Doesn't this askew my roof framing and materials lists?
Seems to me that the 3D reshape tools should do more to reshape objects.