My car is an auto. With all the traffic in Austin I wouldn't have it any other way here. I just learned to drive stick this summer and I will say it is way more fun. As soon as a I graduate and leave Austin my next car will be a stick.
I'm running the pypes mid-muffler system and get a lot of compliments on it. There is some drone though, but that is easily fixed by rolling the windows down and turning the music up.
Go with a C&L cai and tuner from AmericanMuscle. That's what I did and I couldn't be any happier with my choice. Short tubes are totally not worth it either, I learned the hard way. As far as duals, newtakeoff has everything you need with GT mufflers for pretty cheap.