Hi Brian,
Regarding the door problem, please, check this answer I wrote 10 minutes ago (and specially, check the images)
Punchhelpers, "Elevation Editor - trim sticks out under the lower edge?" #7, 12 Jun 2006 7:21 am
You can see also the image attached
Regarding the walls' height, to determine the nature of the problem, the first step is a real map of the situation. To do this, go to the elevation editor and verify the wall heights.
If you set (for example) a wall height of 108", but you set the autofloor in 36", the wall height will be 108"+ 36"= 144"
In the image attached, I set the walls (in both levels) with 96", but the walls of the upper floor have autofloor= 12", therefore the real wall height in the 2nd floor is 108",as you can see
Hope this helps
Patricia