Hello,
I've done the same project and it's all good except some problems with the diff yes.. Did a 1JZ twin turbo manual gear swap and my god.. too fast and powerful .. but the only problem is that you have to weld and cut the body etc. etc. so would take a lot of time and took me 2 weeks straight working with a mechanic to get the engine and gear to be placed right .. the gear housing was a bit a pain in the butt but thank god we found a good one.
The only problem is the differential .. you would either have to swap it with a v6 grand vitara differential or weld the differential so it can be an LSD or a Limited Slip Differential which means 2 tires running at one time rather than having one tire running faster than the other .. it's better for drifting, donuts, etc. but harder to drive in the street because 2 tires would be running at the same time and the steering would be very hard because i doubt you would be able to get the power steering working and the A/c too ..
I did weld mine to an LSD differential and it's running quite good but if you don't want an LSD then go for a v6 differential or one of the following: Mustang differential, Nissan Skyline GTR differential, Mark II, Supra, Soarer, etc. any differential that has been put on a v6 turbo and up engine.
About the gear, I've put a 1JZ Manual gear so 2wd but still powerful in offroading although you need to control the car because too powerful creates less friction and traction so.. if you want a 4x4 don't bother and waste your time putting the stock vitara gear because it would break instantly and we tried it

. Get a 2700 vitara gearbox and do the turning/welding/etc. of the flywheel into the gear so it would be fixed properly between the flywheel, the torque converter and the gear.. any problem would cause a big pain in the butt too..
Overall, it's a pretty hard project but in the end it's all worth it .. I made my car for Skid Pans and drag racing... here are a few videos and I'll be uploading more soon
This video was on 5th gear and low boost so don't think the car is that slow we just wanted to see how the turbo boost opens..
here is a video showing the engine bay and turbo BOV sound hehe.
here I was on the skid pan there were too many cars so I couldn't take my time and do whatever I want plus you would hear the differential at the end of the movie breaking the weld because the weld was not that powerful but it's all fixed now
I hope I helped,
Yamajee.