ANY Suzuki G16 engine can be swapped into a Samurai regardless of the vehicle it comes out of - if it's out of a transverse engined vehicle (Swift, Baleno, Esteem, Cultus, etc.) - it takes a little more work - you need to swap manifolds, modify oil pans, that sort of thing.
If you can get a G16B from a manual transmission 99 it should be a relatively easy swap, if it's an automatic transmission 99, the challenge is going to be the electronics - the transmission controller on the 99 is integrated into the ECU.