There are significant differences between the 2F/3Fs and the 1FZ-FE. However I am told by local mechanics that the H55F transmission (comes with 2F/3F or 2B/3B engine) can be mated to the 1FZ-FE by using locally manufactured housing / adapter plate. There were some reservations on this I read online but from what I can see there is little online from anyone who has actually done this i.e. put the 4500cc 1FZ-FE in a 40 series. Its quite an ambitious project I must say.....
The issue that I foresee with the H151F or the auto A442F transmissions in a 40 series is that these are gigantic transmissions and the engine transmission combo presents a tremendous length when fitted together. This probably would cause issues as there probably will be little room and extreme angle for the rear shaft unless you are increasing the length of the wheelbase. In any case the gears should be ready available from Pehsawar/Quetta and you need some patient research and a sound mechanical team to make sure this is doable.
One thing to check is what diff ratios are you running, your mechanic will be able to tell or simply count ring and pinion teeth, the ratio of which is your final drive ratio, should be either 3.7 (37:10 or locally called das saintees ) or 4.11 (37:9 or Naun saintees). This is important because if the ratios are any higher the vehicle will always feel like a heavy truck even with te 1FZ-FE with very low top speed and short gears. Best if you have 3.7 gears but 4.1 should also work.
You may give some thought to replacing diffs as well possibly to newer Prado TZ ones as these would possibly bring in 4 wheel disc brakes and a very welcome Limited Slip Rear diff. The original 40series diffs are well suited for offroading or loading, but in my experience always feel heavy on the road possibly owing to big size and high weight. Prado diffs would probably be more light and agile and give you the sort of feel that you would want with the 1FZ-FE. Additional cost for two diffs should be around 80K with fitting less the FJ diff chanda that the kabaria may spare you
Anyways, as pointed out patience and research are key here as it is very easy to put all this together but quite tricky to get the optimal result. All the best keep us posted and give a shout if you need any help.