Everywhere I look, it says that the gen 2 alternators are internally regulated whereas the gen 1 is pcm controlled. Could be wrong, but if it is, there's a lot of companies spreading false information.
This has been attempted in the past, usually ends up not working or being limited to working like stock due to the pcm controlling the output. If there was an actual confirmed working drop in replacement, I'd go for it, but from what I can tell, there isn't. As I stated in the beginning, money isn't my concern with this car anymore, is that a bad thing? Probably, but I'm experimenting with this car, seeing what workarounds I can come up with and testing them out myself, which inherently isn't very "cost effective".
Just FYI - I know you are going with a different, high amperage fan. With my gen 1, I put in a gen 2 electric fan from a 2003 model. At first, I used a thermostat to control the fan, and it was all-or-nothing, and in low speed traffic it would start driving the car’s voltage down. I have since changed the fan to one of Oddball’s PWM adaptor boards, and it runs the fan at lower speeds. As a result, the car’s voltage stays above 14v, even with the factory alternator. If your other fan doesn’t work out, you should consider this route.
I seen the board oddball released, I probably would've gone that route if it was out before I put mine in. Mine does alright, putting lower amp fans in would be ideal, but my proform controller is pretty sweet as far as adjustment and speed control goes. I found some mishimoto fans that I think would do pretty good, and they draw almost half the amount of amps my current setup draws.
Note, I'm replacing the fans either way. Derale shrouds are great, but their fans (or mine at least) aren't the greatest. I've already got a bearing squeaking in one of mine. Mishimoto seem to have very high quality products, so I'll be giving them a shot.