Complete 1.6L (harness & ecu) around here are pretty cheap (less than the cost of a 1.3L rebuild kit & machine work). Because the 1.6L is fuel injected, it's much more powerful, and gets BETTER gas mileage than the 1.3L. If you can't afford (or can't find) a 1.6L, you can bolt the 1.6L lower you have to your 1.3L head (people have done it, you just need some special timing belt I think). If you're going to spend the $$$ on a rebuild kit - may as well have the bigger displacement of the 1.6L (much better torque curve).
With 33" tires, carry some front axle spares (buy the double toughs from TT if you can afford them - they're quite nice). You're also going to want some t-case gears. Samurai is unique in that the t-case gears reduce the gearing in high and low range (buy the gears that correct for the 33" tires in hi-range and you'll get 80%ish of your power back - 10-20% will be lost to the increase in rotational mass of the big tires). 2 to 2 1/4" exhaust, headers & high flow cat / muffler will also free a lot of ponies. If you keep your head & intake - the biggest restriction at that point will be your stock carb. Eventually you'll want to swap it for a bigger carb (there's cheap junk yard options from like a 1.8L Toyota), FI, or motorcycle side-draft carb(s). There's always the turbo option, but don't think about it unless you're going FI & have at $1,000-$2,000 to spend on it. If you have some $$$ laying around, the 2.0L is a good swap too.
