I wouldn't say they need a "substantial" overhaul, or even an overhaul at all. On the DL, add a good run-stuffing DT. At LB, build around Ellison, be with Crowell, Fletch, Spikes, or someone like Lance Briggs.
At CB, keep Nate, promote Youboty to 2nd WR, and move McGee back to nickel.