None of these engines is Bolt on fit in Pajero ...specially in Gen1 your choice is very limited because of Gear Box space limitation .
3s is a cheaper solution as you can still find a basic 3S around 50K ...but i recon 5S is a better option.
However 3Ct is a great engine for diesel lovers but its way costly ...a good 3C engine still cost more than 130K .
If you want to stay simple get a good 4D56 with intercooler (japanese one) not of Montero or else than its not a bad engine as one of my friend Taimoor have a 5 door pajero and he is happy .
or you can see my pajero thread to earn some on hand experience.