I was able to fix most of the things you listed. It seems like trying to get the basement walls which are concrete to align with the upper floor is almost impossible. It doesn't help that I'm copying architectural drawings my former contractor made and they aren't exactly perfect.
I couldn't see what the issue was with the handrail.
Fixed the fireplace mantel. I had seen he "explode" option but never clicked it. Thanks!
Fixed the hallway. It was showing as part of the stairwell so I separated that as a room to itself.
However, the ceiling in the living/dining room are still wrong. I'm about to say forget it and just know that I wont be able to see a full camera view that's correct... Frustrating. I appreciate the help.
2nd Adjusted plan 3.zip