I'm not seeing progress in the run game because 3 out of the 4 teams we have played have good defenses. So they scheme the box and dare Kizer to pass. We are also very predictable of when we're going to run. Most times it's 1st and 2nd downs. Against Indy a weaker Defense we got the run going some, but to much to ask against Pittsburgh, Baltimore, and Cincinnati with Burfict back. 

As for why Peppers is playing so far back? I think Gregg lines him up there because he's a Rookie and he still takes a few bad angles in pursuit as well as coverage. So he plays deep to keep everything in front of him. Coming down in that box you have to know when to get back. If you hesitate or take a step in the wrong direction your beat and for a safety that usually means TD for other team.