Since I've owned both, and dragged both, I can give you a little insight.
The srt-10s supposedly pull better times out of the box, but some of the records for fastest 1/4 mile times for stock vipers belong to gen 2's.
I think for drag racing, I actually prefered my gen 2, as the 18 inch rims vs the 19 inch rims (that stock are RUN-FATS) were easier to get a good bite out of. They effectively have a lower gear ratio (gen2) then the gen3s as the switch to 19's makes a difference on over all ratio between transmission/differential and the tire. Then the harder more difficult run craps (which dropping pressure does little good), makes a good aggressive launch a little more difficult then dropping a few pounds in the gen2's stock non-run flats and launching hard.
I also notice I got more wheel hop with the Gen3's then gen2's from hard launches.
Gen 3's should/do trap a higher mile an hour. So I think what you get is relatively close times, but the gen 3's get more mph and the gen2's get better 60 foot times. I think a gen3 with 18 inch rims and non run craps would make up the effective gain the gen2 gets, but its just a guess and the factory will never go backwards.
Transmissions are effectively the same, as the only difference is a solid shaft in 5/6 gear, instead of a 2 part shaft. So no gain there.
Differential is a bit different, and I prefer the gen2 diff over the gen3s. That pump up crap the gen3 does is anoying. The gen2 always seems to have posi ready on the fly.
All and all, I think a gen2 is easier to drag race and look like a champ. A Gen3 with its crappy tires, and questionalble differential prove to be a bit of a challenge. My best 60 foot time is still with a gen2. something like a 1.79 on oem street tires. Gen 3, I got a 1.89 best.
Stock for stock, gen 2 vs gen 3. It will come down to a drivers race. The gen 3 does not have that clear of an advantage. And probably if you do just a 1/8th mile track instead of a 1/4 mile, the gen2 will win more times then not.
My 2 cents.
Jon
Road course racing, FORGET about it, gen 3 all the way.