Ara, its been several centuries since I had a 50/1.4 Nikkor, but the one I had didn't vignette. And I've shot it wide open.
Have you put filters in front of your lens? Lens hood other than the standard issue?
Why do your own tests? These lenses are very well-known. Find a public library that has back issues of Modern Photography or MP on microfilm from the early '70s through about '85 and search for tests of 50/1.4 Nikkors. If that's not practical, they give best sharpness and contrast in the range f/5.6 - f/8.
That said, the concept of "best aperture to shoot at" is pretty fuzzy. Other factors enter, e.g., DoF and shutter speed. FWIW, my practice is not to stop down too far unless max shutter speed available/film speed/illumination for me to or unless I need more DoF. And not to shoot too open unless I need selective focus or circumstances force me to.