This will most likely "not" be the cause of pinholes in the OPs case, but thought I'd mention it for reference. I fought pinholes in the emulsion for quite a while with several different cameras, when using older film holders. Very similar in some respects to the OPs current problem. Pinholes mostly near the edges, etc. After thorough investigation it turned out to be microscopic pieces of grit in the grooves of the film holders. When closing, then opening the the dark-side, the specks of grit would randomly adhere to the film surface. Of course this grit would block light from hitting the emulsion, and leave a microscopic pinhole in the emulsion following development. As I recall, under the correct magnification, angle and lighting conditions, you could see a sunken spot in the dried emulsion where the fixer had done it's work. Ultimately I replaced the cameras and their film holders.