My guess is that has to do with the gear ratios, which are different between the manual and auto boxes. These figs are for the
MCS:
Getrag 6sp MT:
Gears I - VI : 3.308 / 2.130 / 1.483 / 1.139 / 0.949 / 0.816
Final Drive: 3.647
Aisin 6sp AT:
Gears I - VI: 4.044 / 2.371 / 1.556 / 1.159 / 0.852 / 0.672
Final Drive: 3.685
Looks like your answer is right there... the autobox has a MUCH taller 1st gear, and the gap gently tapers off in 2nd - 4th. I'm guessing this is what leads to your slower 0-62 time.
As for the 1/4 mile time: The autobox has an ever so slightly longer final drive ratio, and shorter 5th and 6th gears, so I'm guessing that gives it greater legs than the manual once it gets past 4th gear and closer to the 1/4 mile trap. It probably ends up with a higher trap speed as well.
