You should be fine with the 31x10.50R15's. Hopefully, your TJ came with the 30" tire option - it gives you 15x8" rims. All the other options give you 15x7's (they'll still work for 31's, but not recommended for anything larger like 32's or 33's), except the Sahara, which come std with 16x7's (why!) which opens a whole different can-o-worms. In any case, I'd recommend doing either a 1" body lift, or a coil spacer lift (1"-2") just to gain a little bit of clearance, and a set of sway bar disconnects, if you plan to take it off-road much. As for tires, I'd go with the BFG All-Terrain "KO"'s. They will give you awesome traction and excellent performance on and off road. Plus, they'll last a long time. If you want something more aggressive, you could try the BFG Mud Terrain's, but they don't last as long, and they don't do well on snowy or wet roads. They can't be beat for rocks and mud though. There are some other tires that will outperform these off road, but they tend to be noisy and somewhat unpredictable on road. Hope this helped. Happy Jeepin'!
-Spyder