Choose your lift to accommodate your chosen tire size, but no more. The Samurai is already a narrow, high CG vehicle, and adding a lift increases the center-of-gravity -- not a good thing on the freeway in a crosswind, or when being passed by a semi. Up to about 31" tires you can, and should, stay SPUA (spring UNDER axle), IMHO. Larger tires will necessitate gearing changes as well. The Samurai needs to be geared right for adequate performance. At 60-some HP (new) it's already somewhat underpowered.
For myself, I spend way too much time on the So. Cal freeways, so I chose 29" tires, OME springs and a very small HD shackle lift. Maybe someday I'll go to 30" tires, maybe not. Tires wider than 9.5" would protrude beyond the fender flares, subjecting me to unwanted CHP attention here. The more lift you add, the more unstable the vehicle is likely to be. Do you want to drive to the trails, or is your rig going to be a trailer-queen?
31" tires (10.5" wide) would need about a 3" lift, 8" rims, and extended fender flares, not a direction I want to go for my sometime freeway flyer. More lift may require a dropped pitman arm. Larger tires will make the rig harder to steer. You may want to add power steering from a Sidekick -- I did.