mLongChief

The cause for the 4-stud corning is due to how the studs in that wall were rolled out. One of the studs created while rolling them out landed within the corner of the wall. When this happens, we rotate the stud to make the 4-stud corner, that way there's still a surface on center, despite there not being enough space for the non-rotated stud.
 

 
There's a couple of options you have to change this behavior:
You can change your Wall Connection style for Wall Corners to "Reduced" within the Automatic Framing Defaults Dialog, within the Wall panel. This will prevent the nailer stud from being generated, allowing the problematic corner stud to fit within the wall without needing to rotate. You can change where your stud rollout begins by either using a Framing Reference Point or the Stud Layout settings within the Wall's specification dialog, under its Structure panel. By adjusting the stud rollout, you can move where these studs get built, moving that stud out of the corner so it can fit in the wall without being rotated. You could manually delete the stud, however this would require you to turn off Automatic Wall Framing Hopefully that helps!

It's possible to get the overframing in this case, just takes tweaking the edges of the roof planes to get them into position. Usually when you run into the case of the shoe plates not generating, that means the edge of the roof plane isn't properly seated on the roof plane below it. What I do to get them seated properly is by selecting the edge of the overframed roof that I want a shoe plate along and use either the Place Roof Plane Intersection Point tool or Join Roof Planes tool.
The Place Roof Plane Intersection Point tool works some of the time, but with more complex situations it may not give the exact points I'm looking for. The Join Roof Planes tool works nearly all the time, but it does modify the lower roof plane's edge as well, so I have to move those edges back into place afterwards. It can be a bit tricky getting all the edges in place, but it is possible.
 
OverframedPlan.zip
 

After poking around the plan for a bit, I noticed that the pitch of the truss bases didn't match the pitch of the lower roof. Changing the truss base's pitch to match the lower roof seemed to have fixed it, though I had to redraw the truss base on the right side of the building to get it to work.