Im seriously thinking of using wagoneer springs when I go soa with my yj this summer. Ive done the search and read about it, but I have a few questions. I read that I will need to use lift shackles, for the ones who have done this, what is the shortest or best length shackle to use for this? Im assuming that I would use shackles designed for wagoneers instead of wranglers. Also, is there anything different that I would need to do to the steering since the front axle will be about 2 inches further up?

You can use YJ shackles, I used Currie's Boomerang style. If you are worried about the draglink you can move the tie rod below the springs and use a high steer arm for the draglink.