there's one bigass can of worms... Driven to their fullest, the 5-speed will win. Even with an average driver in each I'd give it to the 5-speed but miss a shift and the auto will win.
My bone stock(stock air filter/stock psi in tires) 02 auto GT coupe ran consistent 14.2's @ 96.5mph in September. I see a lot of times higher than this for stock 01-04 5 speeds without good drivers.
mechanically, a five-speed. they make more power. (less power loss through drive-train) the manuals are also a bit lighter compared to the auto due to the auto's transmission weighing 15-20 pounds more as well as the additional ATF fluid it contains. (about 10 liters extra of fluid compared to a manual;about 20 additional pounds) nothing huge, but every little bit adds up =)