Spring over is the way to go. Using longer shackles is a bad idea, it changes the caster and therefore changes the handling. A good spring over kit from lowrangeoffroad.com or Petroworks.com is the best way to go to run 31's and they give you everything you need to do the lift. The problem is that Samurai springs are usually pretty sacked out (flat or reversed arched), having them re-arched should make the car ride a little better. I would NOT use after market springs to get a better ride on a spring over unless they are stock height, it lifts the car too high and puts the drive shaft in the wrong angle causing you to have to shim the axles to compensate.
Also, to run 31's you should re-gear the car, I used 4.16:1 transfer case gears in my car and I was very happy with the way the car ran and handled both on and off road.