I cannot duplicate these results. I suspect user error. There's a big difference when trying to pull under exposed detail out of shadows where none was captured than shadow noise on a correctly exposed image.
Or, maybe my 5DII is just better than yours? I've not been able to duplicate the black dot phenom either (still on original firmware). My autofocus works well, even in dim light, my battery compartment doesn't creak and the body is free of squeaks and other such. Plus, no focus point light bleed. Hmmm. Guess I'm lucky.