No, for 95 Pajero Mini you'll only have to change differentials. But I would not suggest you to buy 95 Pajero Mini. I drove a few for test drive (95 - 97 with 1100 cc swapped). I felt very annoyed with the noise the engine was making.
One thing you have to understand is that the transmission is "NOT" changed with the engine.. and so the gear changing ratios remain pretty much the same even after the differentials are changed.
So if a 660 cc engine's first gear changes at 10, and second at 20, even if you put a 5000 cc engine, the first gear would still change at 10 and second at 20.
Engine's are basically designed by transmission in mind.. so if you put a 1100cc engine, you should have the same transmission that was designed for 1100cc engine.
I think the newer shape (99 onwards) is more compatible with 660cc because the gear's ratios appear to be much bigger than the previous model.