You can probably make it work with major fender clearancing and tubbing.
You'll probably need to tub out the rear, here are a couple pictures of my partially completed rear tubbing and fender trimming with YJ rear flares:
This is just the first phase I did to avoid cutting up some new 31x10.50 mud tires before a trail run that weekend. I used to run 31x10.50 ATs on different rims (more off-set) that rubbed a little, but I didn't mind the cutting (more siping).
With the new tires and less off-set, I wanted to save the tires so I cut the fenders and added the flares. The flares have a 1/2" lip. Instead of cutting the lip off, and loosing a 1/2" of coverage, I made some spacers out of PVC sheet to slip above the lip and then bolted the assembly to the fender.
When I get back to this project, I will finish the fender cutting, as well as completely removing the wheel wells, and fabricating new taller and slightly deeper wheel wells.
This truck has about 2" or so of lift over stock. There are 1" lift shackles, and maybe about another 1" or so from CJ lift leafs. I replaced two or three of the stock leafs in each pack with one leaf 2" CJ lift leaf (from a 2" CJ lift pack).
I'm going to replace this suspension with full length CJ packs a 1/2" lift shackle set-up, and a 1" body lift. I'm also going to flat fender the front. I'll be doing this by fabricating a new grill (probably stainless steel because I have lots of that at work), and moving the headlights in closer to the rad (lots of room for that on a Samurai).
I'm also expecting to have to tub out the front a bit as well when I replace the 31s with 34x10.50s (maybe Interco LTBs once I see what other people think of this new tire model).
To fit the 31s on your truck, you will have to tub out the front for sure. I'm not sure (off the top of my head) how extensive you will have to go with this, but I garrantee you will have to cut out the hump near the rear of the tire (firewall), and replace it with a deeper formation.
You might consider using CJ or YJ springs for a little lift, and better suspension action.