Although I know losing MacMillan and Gettis really hurt, it was one offensive line position and it wasn't like we threw a freshman in there. I think it hurt the running game more than the passing game,
You are wrong. Josh and James made up the smallest tandem in the middle of the line in the Big Ten BY FAR. Guys basically steamrolled the middle of that line in those games. Stanzi didn't even have time to finish his drop before he had someone in his lap. If James was not an already small center, it might not have been so bad. But, although nasty, size is not his strong suit.
Now, KOK could have realized this and made the necessary adjustments to roll the pocket away from that pressure. But that is asking a bit much.