Sanchez,
I've just recently put a 1UZ into a '95 hilux 2wd double cab and used the W58 supra box.
Some pointers:
You will need to modify your sump (if you have a mid sump that is - if you are blessed with a rear sump, then damn you, lucky bugger).
the steering member fouls 190mm from front of sump. The max vertical clearance from main sump flange is 40mm, so you need to cut a fair chunk out of the alloy and pan.
The main cross member will sit approx 130mm from main sump flange so you will need to cut the pan there too. You will also need to move the oil pick up.
Once you've cut all of this out you will need to make up area somewhere, so you will essentially be making a rear sump.... easiest thing is to go buy one from CRS, $600 may sound expensive, but its cheap unless you have free access to all of the tools - also you will need to send them your oil pick up for exchange.
Engine mounts
I've cadded up the mounts but here is a quick overview: for each engine mount, first you need some 5mm plate. See my basic pic attached - don't take it as gospel, but it will get you on your way.
Getting the engine in
Cut the top radiator mount, this will help you get the motor/gearbox in and out. If you haven't modified the sump, you will need to take the entire sump off. I found that a 130mm high shim spacer made out of wood and sat on the bottom cross member is about the right height for getting the alignment right
Gearbox mounts
If you are keen to cut the gearbox mount, just cut it space it and flip it over. Or just make a full spacer up using the standard mount. I will post some pics.
Engine
Flywheel and clutch: Get a 3S-GTE flywheel of a MR2 Turbo or Celica GT4. Re machine the 8 mounting hole centres, some say flip the ring gear, I have but its tough, and mount the 3S-GTE clutch pack. Make up an adapter plate or buy one - check Quest 4 in Auckland on +64 9 414 1102 they sell them for $250NZD. Mount your slave cylinder off the original bellhousing, just check your clearances off the original engine/gearbox.
Once my fingers recover from all this typing I will continue my rant...
Please, Sideshow, V8Hilux etc, chime in with your comments, even if you have to cut and paste links to the other posts
Muzz