stock manual vs stock auto until the last few years in high end cars like porsche or ferarri manual version is faster. i don't drive a lot of cars fast but i read magazines like motor trend and car and driver and read websites and stuff. when they list times in straight acceleration, like 0-60 and 1/4 mile, the manual is always faster except in the last few years where the technology has gotten better. if mods start coming into the picture the argument is moot because mods muddy the waters up and more variables are introduced.

i don't think you can compare a modded auto transmission or custom torque converters to a stock manual and then say auto is faster in general. those are specific circumstances with custom builds. that would be like a modded gtp beating a stock trans am and then saying grand prixs are faster than trans ams.