I have a 4.5" lifted Samurai with 30" BFGs, 4.625 difs and a Weber-ed 1.6 8-valve that I occasionally drive 26 miles round trip to work. I also occasionally deliver pizza in it. Otherwise OEM drivetrain.
I can maintain 63mph (GPS) at 4,000 RPM on the Interstate with this setup - a mite scary to those unfamiliar with Suzuki engines - with the added bonus of NO constant downshifting! I've been doing that for 7 years on a nominally professionally-remanufactured engine.
If you are looking for comfort and you are over 40, give up now. Even with Tracker seats - which raises the driver enough to make it hard to keep track of overhead traffic signals, the ride is rough. Dropping the tire pressure helps, but mileage also drops and tire wear rises.
Don't let the above comment discourage you, though. I put it there in case you were expecting a ride found in a full-sized pickup truck or a decent car. It's pretty much a given that to consider owning a Samurai, you must have a few screws loose!
A stock 1.3 with 31" tires (disregarding the lift - which, at 5", is too close to the
unmodified stock design limit of 6" for my tastes) will be a big disapointment for you. No engine power combined with the OEM drivetrain (with those big tires) will do a poor job of getting the engine's powerband to match the driving conditions.
Try using a gear calculator to play with tire size and gearing using 3600 RPM as the "meaty spot" for a 1.3 or 1.6 8-valve.
Here is one that I wrote and recommend:
http://www.acksfaq.com/gearcalc-01-04-07.phpIt has many of the commonly-available aftermarket transfercase and differential gearsets built into it.
Play with it and get a feeling of what you are getting into!
I hope that this helps!