Lowdermilk was interviewed after the game and he said they really didn't do anything different in the 2nd half defensively, they just "played better." Remember, Kirk always says it's all about the execution.
For the record, although I wish Ferentz would retire or be fired I don't think he's a horrible coach, just a very mediocre one who has not changed with the times. Kind of like the old guy who refuses to get a cell phone and still insists on using a rotary phone and rabbit ears on his TV.
As for the QB stuff, I don't think Rudock is a bad QB, I just think Beathard is better and gives them a better chance to win. As Miller said in his Instant Reaction, there are things CJ can do that Jake can't, but there isn't anything Jake can do that CJ can't.