Suspension & Tires:
3" of lift is WAY over-kill, and will make for a top-heavy rig. If he's looking for a mall-crawler, or mudder that's fine, but it's crap in real off road situations.
For a lift, use Jeff's coil spacers (cheap), or OME lift (if he's flush with $$$). Calmini's ride quality & longevity (springs, struts & shocks) are CRAP compared to OME. Fender cut from there.
Engine / Drivetrain:
If it's the 1.6L, you'll want to do your typical CIA & high-flow exhaust (2" or 2 1/4") stuff. A 2.0L could benefit from these as well, but won't 'need' it with 31" tires (2.0L is 30% more powerful than 1.6L).
Put 4:1 low-range gears in the t-case. Beef up the straps on the front diff (the housing is aluminum, and doesn't like to move much without breaking), or upgrade to steel front diff (Some Grand Vitaras are steel, Toyota will work, or modified Samurai housing).
Armor & Recovery:
Rock sliders (under door) are a must. Best way is to get 2x4 box tube, cut the area under the door, and re-weld the box tube in place. This keeps stock clearance, and gives great protection. Get front skitds & under-belly, and gas tank armor too, but don't get crazy with the thickness (weight).
Get the tire off the rear door, it won't survive with the weight of 31" M/T. Get a bumper with swing-away carrier (should hold tire, gas tank, and hi-lift at minimum, 2-doors need the storage out there). I like light bumpers (I believe strongly it's the light weight of the Suzuki that gives it's biggest advantages), some people like crazy tank bumpers. Front bumpers look cool, but I'm re-thinking their usefulness. Most are pretty heavy - unnecessarily so. A custom lightweight winch bumper (and cheap harbor freight winch) is the way to fly.
Consider a good cage too. At minimum an extra triangulated sch 40 pipe for the area behind driver / passenger's head (b-pillar I think it is). More if he wants to save the body in a flop / roll.