A picture:
When going to work, I drive out of my neighbourhood and turn 90 degrees onto a main road. With my 2000 hdj100, stock, 4 sp box, I would push the pedal to the metal at standstill, before the turn, and then I would get full power just when the turn is over and I'm aligned on the main road. I tried that, once only, with the 2004 hdj100, 5sp box, and had to compensate halfway through, or end up in the ditch.
There are several changes done on the 5-speed version, not only in the gearbox. The 4sp has one Engine ECU and one Gearbox ECU, while the 5sp has one combined ECU, which makes the communication between engine control and gearchanges much better. The IP and the algorithm controlling it is changed, making it more responsive. The Turbo has a better boost control, which gives power sooner. All in all, the new version feels much snappier, although it is no racer. As an expedition, overland or offroader, it doesn't make much difference though, but the 5sp one is much nicer to drive. There is also the number of airbags to consider, for road use. The 5sp has side airbags, and curtain airbags all the way back to the 3rd row. There are other minor changes as well. One thing that is not better on the 5sp, for the versions without Navi, is the controlpanel for the HVAC. The old one has a very intuitive system, with clear tactile feedback, so that you can easily control everything without looking. The new panel has unreliable pushbuttons where you have to cycle through the settings, and it's not possible to know what you are doing without actually reading the little lcd-display down there. Should have been illegal to design such a system.
Anyhow, both versions get better with a 3" exhaust, but I believe it is more noticable in the old one. There is also the issue with the catalyser, which has a habit of getting blocked, giving the turbo even more delay in spinning up. Also the intake pipes and manifold gets partly blocked by the EGR. So, removing catalyser, egr valve and heater grid, and cleaning out the intake, helps a bit as well.
There is also a modified valve kit available for the auto boxes, from Oz, which makes the shifts snappier.
Reports from Oz, where they really use the cruisers, say that both gearboxes are strong and durable. Exluding the TC of the early years of course (98-2000), but those would be changed long time ago.