I have the same model camera, and a few manual only lenses (M28/2.8, M35/2, M50/2, A50/1.4, M100/4, K200/2.5). I've also had trouble focusing accurately wide open, though I haven't tested as painstakingly as you have.
Here's something I've noticed. The AF indicator seems to be confused by manually focusing. I've focused on the same object at the same distance repeatedly, and considered the lens to be focused when the AF indicator says so. Then, looking at the distance scale on the lens barrel, I can compare what distance the AF sensor chose. It varies by far too much to use a fast lens wide open. Kind of makes fast lenses useless, huh?
As for focusing directly on the ground glass, I find it too difficult since the cameras viewscreen magnification is mediocre (O.K., good by dslr standards) and there's no traditional focusing aid.
I've seen altered split prism screens for sale as a fix online. Maybe that's the way to go? Let me know what develops.
