I've got 31x10's on my YJ now. Never had them rub the front flares, but the rear flare has a nice little arch rubbed in it now. On the stock rims, they rubbed the spring packs on full lock of the steering, so I adjusted the steering stops to stop that. Got some different wheels with better backspacing and was able to put the steering stops back to their original position and get my turning radius back again.
I'd skip the lift shackles if I were you. More trouble than they're worth. They change too many angles, resulting in handling issues and funky tire wear.