Read your edited post: It does not matter about actual or effective focal lengths. You will be measuring the distance of a specific point in the lens (be it the front element, rear element, rear side of shutter or wherever you like) to the formed image (as seen on the ground glass). That distance must be the right film to lens distance.
Not so. Yes, it has to be the right distance, but only god and the lens manufacturer know what that distance is. As stated in my post, the actual lens to film plane distance is not the same thing as the actual physical lens to film plane distance because it depends on the design of the lens. For example, this 500mm lens
http://www.mflenses.com/gallery/v/lensgallery/russian+lens/rubinar500.jpg.html acts like it is several times longer than its physical length, because the thing uses mirrors to fold the light path. If you located this lens with the center of the front lens element 500mm from the film plane, it would be from 3 to 6 times too far away, depending on how many times the light path is folded inside the lens.
While a simple one-element lens with a focal length of 50mm is exactly 50mm from the center of the front element to the film plane, more complex lenses bend the light path and alter the cone dramatically (sometimes the light path converges and sometimes it diverges, only to be brought back to convergence again, and this can happen several times). This takes up space.
To show a really obvious example, retrofocus lenses (what you find on SLRs) focus the light so the light cones converge further back than they do with rangefinder lenses. They do this because they have to compensate for having to focus past the mirror boxes on SLRs. This means they have to be physically more distant from the film plane than would be the case if you were using a non-retrofocus lens of the same focal length, such as is found on a rangefinder.
Even a non-retrofocus 7-element lens of 50mm would have to be located with the center of the front element more physically distant from the film plane than would be the front element of a simpler 3-element lens, because the light path in the 7-element lens converges as a cone and then diverges as an inverted cone several more times on it's way to the rear element than would be the case with a 3-element lens -- and that also requires more space.
In simple terms, a three element 50mm lens on an Agfa Isolette, like an Apotar, is a lot shorter than a 7-element 50mm lens on a Pentax K1000 and needs to be located closer to the film plane too. If you take two dissimilar 50mm lenses, like a 50mm Apotar and a 50mm Pentax SMC, and locate them so the centers of their front elements are the same distance from the film plane, then if the Apotar is about right, the Pentax lens will be way too close.
It was that second post of yours that explained it. Trial and error. You focus the lens for infinity and just move the camera or the lens closer or farther away until it looks like it is in focus,
THEN measure the distance and build your lens board that thick.
