Woodhead,
I did a 37 inch corner install. The block base is 62.5" X 62.5" with a cantilevered area over the base's opening that extends out probably another 8 - 10 inches for the vent floor and landing.
Get some graph paper and draw out your plan to scale. That will help make sense of what space you need. Basically, 39" + 9" (= external size of dome) + whatever insulation you plan (4 - 6 inches) and then space for whatever finish you're going to use (4 - 8"). A 39 inch dome will not fit on my size block base unless you skimp on insulation, which I do not recommend. That means going up an additional 8" in size, to a 70.5" square base, unless you want to attempt cutting cement block.
I think the plans you downloaded use the dimensions for a corner installation based on the pre-fab/casted FB ovens, and are not correct for a brick built version.
I'm not sure of the height of the dome for the lower dome version. 19 -20 inch entry width is fine. 11 - 12" height is also good.
Others, please correct me if I'm steering him wrong.
G.