I think Stamina would have an effect of free throws at the end of a game, since tired player wouldn't shoot as well as a when he's fresh. I wonder if Jump Shot has anything to do with free throws. (IMHO, it should, but only the programmers can say if it is.) I also think height should be a small factor (as I mentioned in a thread many months back), since shorter players have a slightly bigger target (it has to do the shape of the ellipse of the hoop based on the angle of trajectory of the shot on the ball's descent to the basket), but I strongly suspect that height is not a factor (or maybe it's a factor in the FT skill potential, though I doubt that too), but again, only the programmers can say for sure.
Don't ask what sort of Chunks they are, you probably don't want to know. Blowing Chunks since Season 4!