Well, I went with AOD (since it was my first car), but now I am in the process of converting to a manual.
The stick are MUCH faster when the cars are stock or relatively close to. The auto is very consistent (duh), but the stock manual is much faster than the stock AOD. If you replace the AOD and get a stall converter, then that's when you can get the AOD to start competing.
Also, even if the manual was just as slow as the AOD stock, I would still want the manual, because it makes it much more fun to drive.
The stock AOD kills your perf gains from mods. Trust me
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Thanks,
DoranW