They threw way more on first down because Wake Forest has arguably the worst pass defense in the nation. Their head coach literally spent the entire week taking over the secondary so that he could try to help them shore up their shitty defensive back play. ND simply took advantage of their poor secondary and softened up their front by making them commit more players to coverage by exploiting huge weakness. ND will be much more balanced against Stanford, and they'll run more often on first down, not because of Ian Book, but because the opponent calls for more balance.
The game plan against Wake Forest would have been the same with Brandon Wimbush or Ian Book. As you correctly stated, the concern was whether or not Brandon could execute it, which is why it was the perfect week to make the change... Long has called a ton of passing concepts this year that Brandon has simply wasted. Far too often he just locked onto a crosser or a go route because he lacked the confidence to make the easier short or intermediate throw.
Also, in the run game, Long called the same RPOs and read option plays to Book that he did for Wimbush. They were all in the game plan and we saw them all on the field. Book simply makes much better decisions when he's presented with multiple options. Brandon always differed to running the ball because he wasn't confident in his footwork on those RPOs and in the read option game it appeared that he was guessing most of the time. He's such a damn good athlete that when he guessed right he made teams pay, and about half the time when he guessed wrong, but kept, he could still make things happen.