I'm afraid that replacing your factory FI with a carburator would be a seriously expensive mistake, and one you won't be happy with. FI is by far more responsive than either the factory carb or the Weber. Also, if you live in a state with strict emissions testing, the FI system is factory and will normally test better. California, for example, might actually fail the vehicle if the fuel system has been modified from stock.
You might consider flat top pistons for increased compression, possibly bore cylinders .040 over. I honestly don't think you will find that to be a satisfying solution either.
ZOR is producing a Harley Davidson carb setup for the Samurai and it is getting good reviews, though I doubt it would improve on the factory FI. Oh, ZOR is Zuks Off Road.
Realistically, from a bolt on standpoint, you're best bet would be to do as already suggested, let the engine breathe easier. Install a tri-Y header and 2 inch exhaust, using a high flow cat converter (if your state requires one) and a good flowing muffler.
You might also consider changing the gear ratio in the transfer case. Excellent lower ratio gear sets are now available at reasonable cost. These lower gears would improve your 5th gear power. Another approach could be to go to lower differential gears. Doing both would give you outstanding crawl power but that may not be your ultimate goal. If highway mileage and improved power is your goal I would suggest a 4.16:1 gear set for the TC and a good flowing header/exhaust system.