I have a friend with a stock '01 2500 with 315/75R16 Big O XTs, as far as I know they don't rub, if they do, its real minor on the control arms. His truck has the camper and plow packages, and sits higher than most stock ones, it seems.
As far as E rated, many of the oversize tires are D rated, but the actual load rating (in #s) is the same as the stock size E rated; I know that was the case when I went from 245/75 Es to 255/85 D's on mine.
Pete