It is even possible that the return filter (usually in the hydraulic tank, these days) is blocked causing restricted return to tank flow. When you say you checked the filter and it was normal, could you go into how you checked it? If it was me, I would change it to a new filter to insure it was normal.
An infrared heat temp measuring gun should make this a lot easier to troubleshoot, running the pump and shooting the components to see where heat is first being generated.
I would also check to insure no air is being drawn into the line from the hose that feeds the pump from the reserviour, by looking for foam in the hydraulic oil reservoir.
I would be seriously surprised to find any 'improvements' in the mast or lift cylinder size to have any effect in heating, in fact, I would expect it would be contrary, where the larger surface area would dissipate heat from the oil even quicker, with slightly slower lift operation. unless the -pressure- is different.
Are you positive that the pump is not running at speed when it should not be? Does the hydraulic pump "ramp up" when the demand increases, like when lift is selected?