I had to read the post over six times, trying to understand the reasoning. I don't think the flange to film plane distance is relevant for your problem; or perhaps has little to do with hyperfocal distance.
There is no reason why the flange to focal plane distance can be expected to be the same as the lens focal length. The focal length is the distance from the nodal point, or principle plane, to the focal plane. The nodal point can be almost anywhere the designer places it. In a retrofocus lens it can be behind the lens, completely outside the physical space of the lens. In a telephoto lens, it can be out in front of the lens. Or, when there is no requirement for it to be otherwise, it can be somewhere within the lens barrel. In your case, it sounds like the nodal point is outside and behind the lens barrel. None of this is much help for determining hyperfocal distance.
In his book, Optics, Arthur Cox gives Hyperfocal distance as:
H=f + 1000f/N
where H is the hyperfocal distance in inches, f is focal length, and N is the f-number.
It occurs to me that maybe what you wanted to was to determine the lens extension at some hyperfocal distance you have already decided upon. I wonder if that might be best done by experimentation, just because of the difficulty of not knowing where to physically measure to on the lens. But if you need that, I know I can dig it out of Cox's book, since I have been through this before over extension tubes.
Edit: It is clear that Cox is assuming some given size for the circle of confusion, in his formula. He mentions .004 inch in the text. That may or may not do for your purposes.
