There are going to be a few differences between a 92 16V and a 96 16V. The 92 is OBD1 and the 96 is OBD2. So you will need to swap your intake manifold over to the 92 head, so all the 96 wiring will plug in. You will have to swap the 96 distributor over to the 92, since the 96 distributor has the coil built into it, where the 92 doesn't. You will need to swap the 96 oil pump, oil pan and lower timing belt pulley over to the 92 engine, because the 96 has a crank position sensor located on the front of the oil pan, so the oilpan has a hole in the front where the sensor mounts and it reads off the lower timing belt pulley which has "teeth" on it, and the oil pump has a hole in it so the sensor can "see" the teeth on the lower timing belt pulley. You will likely need to swap exhaust manifolds too, since they will be different and the 96 exhaust piping won't directly fit the 92 manifold.
So in short....you will basically only be able to use the block and head of the 92....everything else will need to be swapped from the 96 to the 92.
And as far as swapping a flywheel/clutch onto the back of an engine that originally had an auto behind it.....you just have to remove all the auto tranny stuff (flexplate, torque convertor, etc.) and swap the manual stuff onto it.