From what I've heard... it takes a really good driver in a manual to beat the auto. The auto is capable of shifting quickly, quicker than most drivers of manuals can. So I guess there isn't much of a difference between a well-driven stick and an auto... however, driven well enough, I'd bet manual should be quicker by... two to three tenths?
Auto 5.1 sec 0-60 and 13.6 sec 1/4
Man 5.1 sec 0-60 and 13.5 sec 1/4.
They should be close as the gear ratios are fairly close for the trannys as well. In the past the rear gear and the trannys were vastly different. I do remember reading an article about a late 80's Mustang where this question was asked. The editors were able to, after several runs to find the best conditions, run very closed to the same time in the 1/4 with an auto.