Once the swap is complete, the third floor goes in just like the second.

Since the next floor is going to be recessed, the outside edges of the third floor will need a ceiling to fill in for where the forth floor's floor won't be providing. I added that in this next picture. I elevated it to be .1" lower than the fourth floor's floor so that the fourth floor doesn't show through. I then drew the walls for the study:

The walls are now complete. I decided that the study would be cathedral ceilinged, not needing a flat ceiling (that should have been reflected in the original vertical plan (where the top ceiling thickness was set to 8"), but it makes no difference in the final outcome.
To do the ceilings I used the AS4000 Roof Designer. It does a great job of creating a uniform, well built roof, as long as the exterior wall it is building on are well-defined, and all have uniform top edges at a single elevation. I input the pitch and soffit width parameters and had it build the roof. Comparing the roof's elevation to the table shows we agree on that value.

Back down on the third floor, we need to use the Roof Designer again to do the roofs above the exposed parts of the recessed fourth floor. The Roof Designer does this easily, but It needs to examine both the third floor's walls and the fourth's. So, unless you are working on the topmost roof of a structure, the floor that the roof is being designed for must always be located on the 2nd Punch! floor, so the floor above is available on the fourth. If that is not the case, the Designer won't be able to find the fourth levels walls and will conclude that the current floor is the highest, and will peak the roofs rather than leaving them open.

With that done, the tutorial is complete. In a normal design you would want to go back and add interior walls, furniture, stairs, landscaping and all the rest. As long as the ceiling heights get set as recommended, then new objects should be elevated correctly from the start, with two exceptions. The first is that the proper ceiling heights set the normal elevations to the floor, not a good place to set a table, for example. If you need to temporarily set a different elevation for this reason, set the Design->Set Working Elevation to the exact elevation required; it will stay there until the next floor change, or until it is explicitly reset to something else.
The second exception is for interior walls. Exterior walls, of course, have to always be explicitly elevated according to the table, because they have to include the autofloor. Interior walls may be that mysterious 1/2" off if simply created trusting the Ceiling Height/Working Elevation system. The best bet here is to simply ignore the 1/2 inch problem until you have all the interior walls in place, then run HighRise, click on Back to design, OK, and use the autoSetting features of HighRise to run through the walls and set them correctly. It will lower them all 1/2" if needbe.

HighRise and the contents of this help file are
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