I guess this answers the play calling question.

http://www.mlive.com/wolverines/index.ssf/2015/09/jim_harbaughs_unique_play_call.html#incart_river

This would seem to back what I witnessed the other day rewatching the game.

Drevno stood behind Harbaugh and called something into his headset. Harbaugh heard it, looked at his chart then signaled the play into Jake.

I'm guessing the most in-game input comes from Drevno and Fisch, with less coming from Wheatley and Jay Harbaugh. Those guys are usually coaching up their guys in-between plays.