The thing I ran into, when installing a trackick 2wd tranny in a samurai, was the shortened intermediate shaft ujoints ran at way too steep of angles. I had to remove the small plate off the top of the stock samurai crossmember and drop it down right on the crossmember, so the rear of the tranny would sit lower and the ujoint angles would be acceptable. Not really too hard to do, but something to keep in mind.
Did that raise the front of the motor much? Just wondering about the fan and radiator?
When I installed the 1.6 engine, I used dodge 318 motor mounts, so the engine would sit lower and clear the hood. So by doing that, it made it so the shroud would have to be butchered, in order to fit. I didn't put a shroud back on. It doesn't overheat at all. Oh, I did use a trackick radiator though....so I am not sure if a samurai radiator shroud would have to be butchered much or not. Or if a samurai radiator would cool good enough without a shroud.
Note, that if you do plan on running a trackick radiator that there are a few different widths found in trackicks. Only the narrowest width will fit down between the samurai passengers side frame rail and steering box. You can bolt the trackick radiator in, using both the samurai radiator brackets and the trackick radiator brackets and a spacer between the drivers side bracket and the frame mount.
Here is a pic of how I did the brackets.
It is kinda hard to see in the pics, but what I did was flip the trackick brackets around to the backside of the radiator, made some straps that run from the top of the radiator back to the trackick brackets and bolt the samurai brackets to them.