Just curious, have you driven a GTS or are you going off the rumors of how they will kill you? In accordance to street manner I don't see much of a difference between the later GTS cars and the Gen 3. Both have ABS and neither have stability control. AC cools just fine as well if working properly.
I'm not saying this to talk you out of a Gen3 as they are great cars as well. But if your heart is in a Gen2 then I just want to make sure you've truly vetted out all they truly are.
I'll let the Gen3 owners speak better towards the performance questions you have but all Vipers can be supercharged successfully as long as the tune is good and you don't go crazy with the boost. Tune is key. As with the poster above, I would look into gears for a Gen 2 or Gen 3. I prefer the 3.73's, especially if you go with larger wheels/tires but the 3.55's are a great option too.
98 Red GTS - Borla 2 resonator exhaust (X-pipe in rear), Smooth tubes, K&N filters, Custom Stereo, Forgestar F14 wheels