Congrats on owning a fine lens. I really like mine, and I also have 2 Apo-Rodagons (50mm and 90mm). I was also a little puzzled about mounting it on my D-II at first, and there seem to be three ways of mounting it.
I have it with the conical piece that surrounds the rear cell going through a 2.5" hole in the lensboard (a 4" extension cone) with two screws holding it down from behind the lensboard. Three screws or four would be even better for the purpose of aligning the lens.
If you remove that cone and the rear element, the lens will fit in an ordinary 39mm hole, held in place by the rear element.
There are also 55mm threads on the lens barrel for mounting with a 55mm flange or retaining ring.