Unravel these issues for me please. Wall definition?

[GeneDavis]

This plan is driving me nuts with the behavior I've caused by my worst practice, I'm sure.

 

It is an addition to an uninsulated summer place built a hundred years ago on a shallow stone foundation.  The new addition will get a proper foundation.  Rainscreen siding detail for walls so as to be able to get siding to cover concrete stemwall.

 

I cannot figure out how I messed this up.  It would not frame as expected, so I did the floor frame manually.

 

The remaining issues I have are as shown in the images.  Insulation won't show in 2D or 3D where it is on the upper half of the pony wall foundation.  A gap in the exterior layers won't close where the mudsill is.

 

I can just CAD patch to fix this enough to do the con docs, but it annoys me I cannot solve this riddle.

Bedroom bath addition no steps (2).zip