Replying to Adjust Wall Surface to...

Set the new lower sill plate to be 0'-0" wide and make sure it references the outside edge of the bearing part of the walls.

If you want to have the siding hang down below the stone/bottom of floor system, you can cheat it by setting a sill plate that is offset below the joists/sill plate. Or, create a wall assembly with a transition for the siding and sheathing as you want.

Why is your subfloor not out to the edge of the rim joist? If you adjust/clean up that your siding and wall will clean up better.

And here is the photo intended to be with this text: But here you can see that, with the left wall, I am fine if the siding from the main floor wall covers the entire joist set distance, which it does with the "cover floor" command. But here too, I'd actually want the siding to cover an inch or so more of stone...

This is the photo that was supposed to go with this text: Here is a cross section view--you can see the sill plate, and how I just want the main floor wall siding to come over that sill plate, and maybe a little bit further over the stone.

Here is the photo--I forgot to attach.

Here's the photo--the others didn't attach...

Make sure you have a "Sill Plate" if its a wood floor system.

But here you can see that, with the left wall, I am fine if the siding from the main floor wall covers the entire joist set distance, which it does with the "cover floor" command. But here too, I'd actually want the siding to cover an inch or so more of stone...

Here is a cross section view--you can see the sill plate, and how I just want the main floor wall siding to come over that sill plate, and maybe a little bit further over the stone.