Transgo -2 usually retains the automatic shift functions of the stock valve body, but improves the shifts. There should be a "shift command" option if it's a Chrysler transmission, but I dont' think it's needed on the Ford and Chevys.
If the "Stage 2" is referring to the transmission you're on your own. It's probably some BS a trans shop or company uses to describe their pricing options.
Later,
Greg