I used to have the same damn problem when I first bought my car and it was just barely broken in, id say around 1000 miles on the clock, but I wasnt necessarily emergency stopping, I would just come up to a red light on my way to work in the mornings with the clutch pressed in and it would stumble bad then pick back up, i can remember on one accasion the battery light popped on, it did it at the same damn light every morning too and after that it was fine the rest of the day, it quit probably about 2 weeks after it started doing it. I think about the only mod I had was the injen, but cant exactly remember its been so long and now I have 17K on the car.
Mike