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What gearbox should go in / Transfer case?
The late 1.0 transfer case you have will be ideal.
You will need a 1.3 Sierra gearbox and a 1.6 adapter plate, or a Vitara gearbox.
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Tail shaft and gear issues?
No. No need to move the transfer case regardless of gearbox choice. You will need a 1.3 jackshaft or have a 1.3 jackshaft modified depending on gearbox choice.
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Fuel Pumps?
You're haven't specified engine variant. Most 1992 Vitaras are carby, only the "estate wagon" (LWB) vitaras were EFI. If the engine is carby, the mechanical pump on the engine is all that's required. If it's EFI, you'll need an EFI fuel system, generally an SJ80 coil sierra tank with a vitara swimmer pump is ideal, or, you can modify fuel tank mounts to accept a Vitara SWB EFI tank.
There are also external pump options but they're inferior for various reasons.
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Wiring / ECU Issues?
If you have an EFI G16, you'll need the engine loom and ECU from the correct variant of car for the motor (there are three variants of EFI G16, not counting the TBI Escudo motor that pops up from time to time) you'll need to add a VSS and check engine light to your dashboard, and a couple of relays. If you don't have this as part of the deal, you're in for a world of hurt as you'll need to find an early EFI vitara to get the right ECU and loom.
If it's a carby motor then wiring is pretty straightforward. You will also need to delete the external voltage regulator which sits on the passenger side inside the car. (regardless of whether the engine is carby or EFI)
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Mounts for Engine and Gearbox?
Engine mounts need to be moved. they are in a completely different position in the SJ410. Gearbox mount will need modification.
All up it's a pretty sizeable job and will depend a lot on what comes on the pallet with the G16.