Correct, that's why I referred him to the first gen swap page. Outlines how to handle the mechanics of the swap as they will be identical. Clutch pedal/skinny brake is fairly easy to install, the hole is cut for the master cylinder so that is bolt in which will include the reservoir and hydraulic line to the slave, there is a block off plate on the floor that is simple to remove and either cut a hole for the shifter or swap the 5 speed one over. You will also need the manual trans starter as it's different.
The difference will come down to how it's wired. The first gen is simple as pie as the trans harness is separate from the engine harness and is a matter of 4 connectors to change. The clutch switch(included with a new master) plugs into a harness under the dash. Again in the first gen this is wired in regardless if you have an auto or a manual. A resistor is just placed in it if you have an auto. I don't know if the second gens are similar or not.
I will reiterate that if you can find a complete donor this would be a fairly straight forward swap. It may seem intimidating at first but after completing one I would feel very confident in saying this is a weekend swap if you have all the parts a head of time.