Engine rebuild

I am doing a engine rebuild on a 2002 isuzu trooper and the tech manual instructs to remove the transmision first? I did a tranny job on a rodeo and that was not fun! Is there any reason the tranny has to come out to pull the engine on this trooper?? also will a 3.2L v-6 fit in the place of this 3.5L v-6 which is notorius for throwing the rods and crankshaft

With some vehicles it is easier to remove the engine with the trans off. With others, you can leave the trans in place. Generally, you have to be able to “swing” the whole package further forward with the trans attached so instead of pulling off the transmission, you might have to take out the radiator, AC condenser and some coolers instead. A lot of times people use the latter procedure when they are replacing both the engine and trans with salvaged parts.

If no one here has the experience with ca. 2002 Troopers, I would suggest that you go to an active Trooper board or two. That is especially true for the engine swap. There are no factory procedures for heterologous engine swaps. They are SOTP and some of them end up being easy and some are next to impossible. If someone has tried it, you really want to find them and see what their experience is.