Saad,
Thanks for the additional details.
The symptoms you describe (hits hard on small bumps, ok but not great on large ones *and* only 7 gradation changes of fluid between high and low) are usually what happens when the four damping spheres are low. Normally if you replace the spheres you should see roughly 13 gradation changes (+/-).
When the spheres are running low then they will be partially filled with fluid even at the low suspension setting because they just don't have the pressure to fully expand. Then when pressure is further increased to raise the truck higher they fill to the remaining capacity. Ergo only a small change in fluid level at the tank. With properly charged (usually meaning new) spheres the high pressure keeps the spheres almost empty of fluid at low and they can accept more as the truck is raised so there is a larger change at the tank.
The rest of the system can affect ride quality as well but not as much. The system is essentially all hydraulic so you would next look for restrictions at the various fluid fittings e.g.: are the actuators stuck in a wrong position that restricts flow, are the shock ports and lines connected right, any bypass or press release valves not opening right so they restrict flow, etc. That does not sound like it is occurring.
Also note that the 'shocks' on the AHC are not really shock dampers like on a regular suspension, they are simply hydraulic rams. They pass the shock right on through to the Damping Spheres similar to a remote reservoir system (but adaptable and computer controlled). This means that replacing the spheres on these trucks is the same as replacing shocks on a standard car (but easier on ours). Unless they are leaking fluid the actual shock rams should not ever need replacing.
The raise and lower times seem about right; maybe a little slow but not much. Toyota designed the system for durability and comfort so it moves slow and smooth rather than rapidly like one of the competition hydro cars that hop

Anyway, if your times up and down were ridiculously long then that would suggest a problem with the central (main) accumulator cylinder or the pump system somewhere. Yours is probably fine.
On net this raises question about your spheres:
1) Did you use factory new damping spheres? Is it possible that someone swapped in used ones and thought you might not notice or did you use a set from a breaker maybe?
2) Are you sure they were actually replaced? I.e. maybe the shocks were replaced but not the spheres or the actuators were replaced but not the spheres?
3) Did you use LHM+ or Toyota AHC fluid to refill the system? My thinking here is that *if* you used brake fluid or something else by accident that it might dissolve the diaphragms after a few weeks causing the globes to fail. This takes a little time though so it would not likely show immediately
Or, as Art (agaisin) mentioned earlier, is the truck *really* overweight? If it is either overweight or jacked up too high the new spheres might behave like old ones because of massive overloading. I doubt this is the case for you since you have not mentioned anything about having an extra 500 kilos of static load =)
First thoughts. I'll see if I can think of alternate explanations.