This ^^ took me weeks to nail down when to sprint and when not to sprint. But once I got that down I felt like a new man in the run game.
Also are you using the generic 49'ers playbook? I really recommend creating your own. I have a LOT of success running with Crowell and the Browns in a spread offense running inside zones and traps. I play on All-Madden with Run Blocking at 40 and CPU Tackling at 57 and consistently put up 150 yards on the ground.
Try attacking the A gaps (gap between the center and the guard on each side of the line) in spread formations on inside zone and dive plays , it's usually money every time.