I would think the 2JZ-GE (not the turbo charged GTE!) in an FJ40 should be fine enough if you mate it to the original gearbox and diffs. Plenty of 2JZ conversions in CJ7s/CJ5s by now though not many perhaps in FJ40s because of various reasons. Fuel economy is a good reason of swapping 2F with 2JZ even though its not the best match for the drivetrain...
The FJ40 gears and axles are quite heavy and bulky and though it will be a very fast car, it will not be tremendously overpowered. On the contrary, the heavy drivetrain would put the 2JZ to a challenge and life expectancy of the engine and parts may not be comparable to a slightly bigger engine. 4 wheel disk brakes and 31 inch tires with wide/backspaced rim would be a must!