Ray,
thanks for digging out those guidelines of S/N>40 for exellent image quality, >10 for aceptable, they at least set upper limits on dynamic range at various ISO's.
For example, to get above S?N of 40, you have to count 40 squared = 1600 electrons just to get above shot noise. Other noise sources are comfortably less than 40 electrons under normal circumstances I believe, so you are probably OK at that level. Digging one more number out of Kodak's site, of about 50,000 electrons as the maximum that several of their DSLR sensors can count, and you have a typical dynamic range of 1600 to 50,000, a ratio of 30 or five stops; (close to transparency film?).
Probably in shadows that are more than five stops from the top (which are even hard to print without compressing contrast), the more liberal "acceptable level" is often all you can make out, and that lets you go down to 100 electrons, which suggests a dynamic range of 9 stops. This at least fits with figures in the range 8 to 9 stops I have seen is some technical articles that, however, are vague about their definitions of dynamic range.
Every stop higher ISO loses one stop at the top of the range, so loses one stop of dynamic range for high contrast subjects.
As to when ISO pushing is applied, it seems from the Roper Scientific reference that the traditional place is gain in the amplifier feeding the A/D converter, with some sensors also doing something with "on-chip" gain; in either case, before A/D conversion. I have not heard any mention of any camera doing it in the digital domain (despite my earlier speculations).